2024-03-28T14:52:29Z
https://zenodo.org/oai2d
oai:zenodo.org:3629604
2020-01-29T07:20:52Z
user-cami
openaire_data
Meyer, Fernando
2020-01-28
<p>Taxonomic binning of the gold standard pooled assembly<br>
<strong>Software: </strong>CAT<br>
<strong>SoftwareVersion: </strong>4.6<br>
<strong>DataURL: </strong> https://data.cami-challenge.org/participate<br>
<strong>SoftwareURL:</strong> https://github.com/dutilh/CAT<br>
<strong>ReferenceDatabase:</strong> prebuilt 2018-12-12<br>
<strong>Taxonomy:</strong> NCBI 2018-12-12<br>
<strong>ShortReadsUsed:</strong> False<br>
<strong>LongReadsUsed:</strong> False<br>
<strong>CommandUsed:</strong> CAT contigs -c anonymous_gsa_pooled.fasta -d CAT_prepare_20181212/2018-12-12_CAT_database/ -t CAT_prepare_20181212/2018-12-12_taxonomy/ --tmpdir tmp --nproc 16</p>
https://doi.org/10.5281/zenodo.3629604
oai:zenodo.org:3629604
Zenodo
https://zenodo.org/communities/cami
https://doi.org/10.5281/zenodo.3629603
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
metagenomics
taxonomic binning
CAMI 2 Mouse Gut Toy data set
CAT 4.6 taxonomic binning of the CAMI 2 Mouse Gut Toy data set, gold standard pooled assembly
info:eu-repo/semantics/other
oai:zenodo.org:3629567
2020-01-29T07:20:52Z
user-cami
openaire_data
Meyer, Fernando
2020-01-28
<p>Biobox YAML file for the CAMI 2 Mouse Gut Toy data set, samples 0-63</p>
https://doi.org/10.5281/zenodo.3629567
oai:zenodo.org:3629567
Zenodo
https://zenodo.org/communities/cami
https://doi.org/10.5281/zenodo.3629566
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
metagenomics
bioboxes
CAMI 2 Mouse Gut Toy data set
Biobox YAML file for the CAMI 2 Mouse Gut Toy data set, samples 0-63
info:eu-repo/semantics/other
oai:zenodo.org:3629628
2020-01-29T07:20:52Z
user-cami
openaire_data
Meyer, Fernando
2020-01-28
<strong>Software: </strong>MetaPalette<br><strong>SoftwareVersion: </strong>1.0.0<br><strong>DataURL: </strong> https://data.cami-challenge.org/participate<br><strong>SoftwareURL:</strong> https://doi.org/10.5281/zenodo.1730624<br><strong>DockerImage:</strong> stefanjanssen/docker_profiling_tools:commonkmers<br><strong>IsBiobox:</strong> True<br><strong>BioboxYAMLFile:</strong> https://zenodo.org/record/3629567/files/biobox.yaml?download=1<br><strong>ReferenceDatabase:</strong> https://zenodo.org/record/1749272<br><strong>ShortReadsUsed:</strong> True<br><strong>LongReadsUsed:</strong> False<br><strong>CommandsUsed:</strong> docker run \<br>--volume="/path/to/19122017_mousegut_scaffolds_yaml:/bbx/mnt/yaml:ro" \<br>--volume="/path/to/19122017_mousegut_scaffolds:/bbx/mnt/input:ro" \<br>--volume="/path/to/output:/bbx/mnt/output:rw" \<br>--volume="/path/to/output/metadata:/bbx/metadata:rw" \<br>--volume="/path/to/output/cache:/cache:rw" \<br>--volume="/path/to/reference_database:/exchange/db:rw" \<br>stefanjanssen/docker_profiling_tools:commonkmers
https://doi.org/10.5281/zenodo.3629628
oai:zenodo.org:3629628
Zenodo
https://zenodo.org/communities/cami
https://doi.org/10.5281/zenodo.3629627
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
metagenomics
taxonomic profiling
CAMI 2 Mouse Gut Toy data set
MetaPalette 1.0.0 taxonomic profiling of the CAMI 2 Mouse Gut Toy data set, samples 0-63
info:eu-repo/semantics/other
oai:zenodo.org:5006866
2022-01-21T18:43:24Z
user-cami
openaire_data
Meyer, Fernando
2021-06-21
<p>Taxonomic profiles including participant submissions for the CAMI 2 Challenge datasets: marine, plant-associated, strain madness.</p>
<p>See <a href="https://www.microbiome-cosi.org/cami">https://www.microbiome-cosi.org/cami</a> and <a href="https://data.cami-challenge.org/participate">https://data.cami-challenge.org/participate</a>.</p>
https://doi.org/10.5281/zenodo.5006866
oai:zenodo.org:5006866
Zenodo
https://zenodo.org/communities/cami
https://doi.org/10.5281/zenodo.5006865
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Taxonomic profiles of the CAMI 2 Challenge datasets: marine, plant-associated, strain madness
info:eu-repo/semantics/other
oai:zenodo.org:3629630
2020-01-29T07:20:52Z
user-cami
openaire_data
Meyer, Fernando
2020-01-28
<strong>Software: </strong>TIPP<br><strong>SoftwareVersion: </strong>2.0.0<br><strong>DataURL: </strong> https://data.cami-challenge.org/participate<br><strong>SoftwareURL:</strong> https://github.com/smirarab/sepp<br><strong>DockerImage:</strong> stefanjanssen/docker_profiling_tools:tipp<br><strong>IsBiobox:</strong> True<br><strong>BioboxYAMLFile:</strong> https://zenodo.org/record/3629567/files/biobox.yaml?download=1<br><strong>ReferenceDatabase:</strong> 2015<br><strong>ShortReadsUsed:</strong> True<br><strong>LongReadsUsed:</strong> False<br><strong>CommandsUsed:</strong> docker run \<br>--volume="/path/to/19122017_mousegut_scaffolds_yaml:/bbx/mnt/yaml:ro" \<br>--volume="/path/to/19122017_mousegut_scaffolds:/bbx/mnt/input:ro" \<br>--volume="/path/to/output:/bbx/mnt/output:rw" \<br>--volume="/path/to/output/metadata:/bbx/metadata:rw" \<br>--volume="/path/to/output/cache:/cache:rw" \<br>stefanjanssen/docker_profiling_tools:tipp
https://doi.org/10.5281/zenodo.3629630
oai:zenodo.org:3629630
Zenodo
https://zenodo.org/communities/cami
https://doi.org/10.5281/zenodo.3629629
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
metagenomics
taxonomic profiling
CAMI 2 Mouse Gut Toy data set
TIPP 2.0.0 taxonomic profiling of the CAMI 2 Mouse Gut Toy data set, samples 0-63
info:eu-repo/semantics/other
oai:zenodo.org:10728160
2024-03-01T06:34:03Z
user-cami
openaire
user-nfdi4microbiota
Meyer, Fernando
Fritz, Adrian
McHardy, Alice C.
2022-07-10
<p>Poster presented by Fernando Meyer at the 30th Conference on Intelligent Systems for Molecular Biology (ISMB 2022), July 10-14, 2022, in Madison, USA.</p>
<p>The Critical Assessment of Metagenome Interpretation (CAMI) is an initiative for the evaluation of methods for metagenome analysis through community involvement in the design of benchmark datasets, evaluation procedures, choice of performance metrics and questions to focus on. The first CAMI challenge delivered insights into the performances of metagenome assembly, genome and taxonomic binning and profiling programs across multiple complex benchmark datasets, including unpublished genomes. In the second round of challenges (CAMI II), we assessed program performances and progress on even larger and more complex datasets sampled from ~1,700 genomes and ~600 circular elements, including long-read data and further performance metrics such as runtime and memory use.</p>
https://doi.org/10.5281/zenodo.10728160
oai:zenodo.org:10728160
Zenodo
https://zenodo.org/communities/cami
https://zenodo.org/communities/nfdi4microbiota
https://doi.org/10.5281/zenodo.10728159
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
ISMB, 30th Conference on Intelligent Systems for Molecular Biology, Madison, USA, 10-14 July, 2022
Critical Assessment of Metagenome Interpretation: the second round of challenges
info:eu-repo/semantics/conferencePoster
oai:zenodo.org:3629588
2020-01-29T07:20:51Z
user-cami
openaire_data
Meyer, Fernando
2020-01-28
Genome binning of the gold standard pooled assembly <br><strong>Software: </strong>MaxBin<br><strong>SoftwareVersion: </strong>2.2.7<br><strong>DataURL: </strong> https://data.cami-challenge.org/participate<br><strong>SoftwareURL:</strong> https://sourceforge.net/projects/maxbin/<br><strong>DockerImage:</strong> cami/maxbin:2.2.7<br><strong>IsBiobox:</strong> No<br><strong>ShortReadsUsed:</strong> True<br><strong>LongReadsUsed:</strong> False<br><strong>CommandUsed:</strong> run_MaxBin.pl -thread 16 -contig anonymous_gsa_pooled.fasta -out output -reads sample_0/reads/anonymous_reads.fq -reads2 sample_1/reads/anonymous_reads.fq -reads3 sample_2/reads/anonymous_reads.fq -reads4 sample_3/reads/anonymous_reads.fq -reads5 sample_4/reads/anonymous_reads.fq -reads6 sample_5/reads/anonymous_reads.fq -reads7 sample_6/reads/anonymous_reads.fq -reads8 sample_7/reads/anonymous_reads.fq -reads9 sample_8/reads/anonymous_reads.fq -reads10 sample_9/reads/anonymous_reads.fq -reads11 sample_10/reads/anonymous_reads.fq -reads12 sample_11/reads/anonymous_reads.fq -reads13 sample_12/reads/anonymous_reads.fq -reads14 sample_13/reads/anonymous_reads.fq -reads15 sample_14/reads/anonymous_reads.fq -reads16 sample_15/reads/anonymous_reads.fq -reads17 sample_16/reads/anonymous_reads.fq -reads18 sample_17/reads/anonymous_reads.fq -reads19 sample_18/reads/anonymous_reads.fq -reads20 sample_19/reads/anonymous_reads.fq -reads21 sample_20/reads/anonymous_reads.fq -reads22 sample_21/reads/anonymous_reads.fq -reads23 sample_22/reads/anonymous_reads.fq -reads24 sample_23/reads/anonymous_reads.fq -reads25 sample_24/reads/anonymous_reads.fq -reads26 sample_25/reads/anonymous_reads.fq -reads27 sample_26/reads/anonymous_reads.fq -reads28 sample_27/reads/anonymous_reads.fq -reads29 sample_28/reads/anonymous_reads.fq -reads30 sample_29/reads/anonymous_reads.fq -reads31 sample_30/reads/anonymous_reads.fq -reads32 sample_31/reads/anonymous_reads.fq -reads33 sample_32/reads/anonymous_reads.fq -reads34 sample_33/reads/anonymous_reads.fq -reads35 sample_34/reads/anonymous_reads.fq -reads36 sample_35/reads/anonymous_reads.fq -reads37 sample_36/reads/anonymous_reads.fq -reads38 sample_37/reads/anonymous_reads.fq -reads39 sample_38/reads/anonymous_reads.fq -reads40 sample_39/reads/anonymous_reads.fq -reads41 sample_40/reads/anonymous_reads.fq -reads42 sample_41/reads/anonymous_reads.fq -reads43 sample_42/reads/anonymous_reads.fq -reads44 sample_43/reads/anonymous_reads.fq -reads45 sample_44/reads/anonymous_reads.fq -reads46 sample_45/reads/anonymous_reads.fq -reads47 sample_46/reads/anonymous_reads.fq -reads48 sample_47/reads/anonymous_reads.fq -reads49 sample_48/reads/anonymous_reads.fq -reads50 sample_49/reads/anonymous_reads.fq -reads51 sample_50/reads/anonymous_reads.fq -reads52 sample_51/reads/anonymous_reads.fq -reads53 sample_52/reads/anonymous_reads.fq -reads54 sample_53/reads/anonymous_reads.fq -reads55 sample_54/reads/anonymous_reads.fq -reads56 sample_55/reads/anonymous_reads.fq -reads57 sample_56/reads/anonymous_reads.fq -reads58 sample_57/reads/anonymous_reads.fq -reads59 sample_58/reads/anonymous_reads.fq -reads60 sample_59/reads/anonymous_reads.fq -reads61 sample_60/reads/anonymous_reads.fq -reads62 sample_61/reads/anonymous_reads.fq -reads63 sample_62/reads/anonymous_reads.fq -reads64 sample_63/reads/anonymous_reads.fq
https://doi.org/10.5281/zenodo.3629588
oai:zenodo.org:3629588
Zenodo
https://zenodo.org/communities/cami
https://doi.org/10.5281/zenodo.3629587
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
metagenomics
genome binning
CAMI 2 Mouse Gut Toy data set
MaxBin 2.2.7 genome binning of the CAMI 2 Mouse Gut Toy data set, samples 0-63, gold standard pooled assembly
info:eu-repo/semantics/other
oai:zenodo.org:3629590
2020-01-29T07:20:52Z
user-cami
openaire_data
Meyer, Fernando
2020-01-28
Genome binning of the gold standard pooled assembly <br><strong>Software: </strong>MetaBAT<br><strong>SoftwareVersion: </strong>2.12.1<br><strong>DataURL: </strong> https://data.cami-challenge.org/participate<br><strong>SoftwareURL:</strong> https://bitbucket.org/berkeleylab/metabat<br><strong>ShortReadsUsed:</strong> True<br><strong>LongReadsUsed:</strong> False<br><strong>CommandUsed:</strong> bowtie2-build anonymous_gsa_pooled.fasta anonymous_gsa_pooled.fasta<br>for i in {0..63}; do bowtie2 -q --threads 30 --fr -x anonymous_gsa_pooled.fasta --interleaved sample_${i}/anonymous_reads.fq -S anonymous_reads_sample_${i}.sam ; done<br>for i in {0..63}; do samtools view -b sample_${i}.sam -o anonymous_reads_sample_${i}.bam & done<br>for i in {0..63}; do samtools sort anonymous_reads_sample_${i}.bam -o anonymous_reads_sample_${i}.sorted.bam ; done<br>for i in {0..63}; do samtools index anonymous_reads_sample_${i}.sorted.bam ; done<br>runMetaBat.sh -l anonymous_gsa_pooled.fasta anonymous_reads_sample_*.sorted.bam
https://doi.org/10.5281/zenodo.3629590
oai:zenodo.org:3629590
Zenodo
https://zenodo.org/communities/cami
https://doi.org/10.5281/zenodo.3629589
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
metagenomics
genome binning
CAMI 2 Mouse Gut Toy data set
MetaBAT 2.12.1 genome binning of the CAMI 2 Mouse Gut Toy data set, samples 0-63, gold standard pooled assembly
info:eu-repo/semantics/other
oai:zenodo.org:4964422
2022-01-21T18:41:53Z
user-cami
openaire_data
Meyer, Fernando
2021-06-16
<p>Genome binnings including participant submissions for the CAMI 2 Challenge datasets: marine, plant-associated, strain madness.</p>
<p>See <a href="https://www.microbiome-cosi.org/cami">https://www.microbiome-cosi.org/cami</a> and <a href="http://data.cami-challenge.org/participate">https://data.cami-challenge.org/participate</a>.</p>
https://doi.org/10.5281/zenodo.4964422
oai:zenodo.org:4964422
Zenodo
https://zenodo.org/communities/cami
https://doi.org/10.5281/zenodo.4964421
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Genome binnings of the CAMI 2 Challenge datasets: marine, plant-associated, strain madness
info:eu-repo/semantics/other
oai:zenodo.org:3629614
2020-01-29T07:20:52Z
user-cami
openaire_data
Meyer, Fernando
2020-01-28
<strong>Software: </strong>Bracken<br><strong>SoftwareVersion: </strong>2.5<br><strong>DataURL: </strong> https://data.cami-challenge.org/participate<br><strong>SoftwareURL:</strong> https://github.com/jenniferlu717/Bracken<br><strong>DockerImage:</strong> cami/bracken:2.5<br><strong>IsBiobox:</strong> True<br><strong>BioboxYAMLFile:</strong> https://zenodo.org/record/3629567/files/biobox.yaml?download=1<br><strong>ReferenceDatabase:</strong> Kraken standard db built May 2019<br><strong>ShortReadsUsed:</strong> True<br><strong>LongReadsUsed:</strong> False<br><strong>CommandsUsed:</strong> docker run \<br>--volume="/path/to/19122017_mousegut_scaffolds_yaml:/bbx/mnt/yaml:ro" \<br>--volume="/path/to/19122017_mousegut_scaffolds:/bbx/mnt/input:ro" \<br>--volume="/path/to/output:/bbx/mnt/output:rw" \<br>--volume="/path/to/output/metadata:/bbx/metadata:rw" \<br>--volume="/path/to/output/cache:/cache:rw" \<br>cami/bracken:2.5
https://doi.org/10.5281/zenodo.3629614
oai:zenodo.org:3629614
Zenodo
https://zenodo.org/communities/cami
https://doi.org/10.5281/zenodo.3629613
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
metagenomics
taxonomic profiling
CAMI 2 Mouse Gut Toy data set
Bracken 2.5 taxonomic profiling of the CAMI 2 Mouse Gut Toy data set, samples 0-63
info:eu-repo/semantics/other
oai:zenodo.org:4982288
2022-01-21T18:42:54Z
user-cami
openaire_data
Meyer, Fernando
2021-06-18
<p>Taxonomic binnings including participant submissions for the CAMI 2 Challenge datasets: marine, plant-associated, strain madness.</p>
<p>See <a href="https://www.microbiome-cosi.org/cami">https://www.microbiome-cosi.org/cami</a> and <a href="https://data.cami-challenge.org/participate">https://data.cami-challenge.org/participate</a>.</p>
https://doi.org/10.5281/zenodo.4982288
oai:zenodo.org:4982288
Zenodo
https://zenodo.org/communities/cami
https://doi.org/10.5281/zenodo.4982287
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Taxonomic binnings of the CAMI 2 Challenge datasets: marine, plant-associated, strain madness
info:eu-repo/semantics/other
oai:zenodo.org:3629592
2020-01-29T07:20:52Z
user-cami
openaire_data
Meyer, Fernando
2020-01-28
Genome binning of the gold standard pooled assembly <br><strong>Software: </strong>CONCOCT<br><strong>SoftwareVersion: </strong>1.0.0<br><strong>DataURL: </strong> https://data.cami-challenge.org/participate<br><strong>SoftwareURL:</strong> https://github.com/BinPro/CONCOCT<br><strong>DockerImage:</strong> quay.io/biocontainers/concoct:1.0.0--py37h88e4a8a_5<br><strong>IsBiobox:</strong> No<br><strong>ShortReadsUsed:</strong> True<br><strong>LongReadsUsed:</strong> False<br><strong>CommandUsed:</strong> for i in {0..63}; do bowtie2 -q --threads 30 --fr -x anonymous_gsa_pooled.fasta --interleaved sample_${i}/anonymous_reads.fq -S anonymous_reads_sample_${i}.sam ; done<br>for i in {0..63}; do samtools view -b sample_${i}.sam -o anonymous_reads_sample_${i}.bam & done<br>for i in {0..63}; do samtools sort anonymous_reads_sample_${i}.bam -o anonymous_reads_sample_${i}.sorted.bam ; done<br>for i in {0..63}; do samtools index anonymous_reads_sample_${i}.sorted.bam ; done<br>cut_up_fasta.py anonymous_gsa_pooled.fasta -c 10000 -o 0 --merge_last -b contigs_10K.bed > contigs_10K.fa<br>concoct_coverage_table.py contigs_10K.bed /host/benchmarking/fmeyer/output/bowtie2/mouse_gut/sorted_bam/anonymous_reads_sample_*.sorted.bam > coverage_table.tsv<br>concoct --composition_file contigs_10K.fa --coverage_file coverage_table.tsv -b<br>merge_cutup_clustering.py clustering_gt1000.csv > clustering_merged.csv
https://doi.org/10.5281/zenodo.3629592
oai:zenodo.org:3629592
Zenodo
https://zenodo.org/communities/cami
https://doi.org/10.5281/zenodo.3629591
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
metagenomics
genome binning
CAMI 2 Mouse Gut Toy data set
CONCOCT 1.0.0 genome binning of the CAMI 2 Mouse Gut Toy data set, samples 0-63, gold standard pooled assembly
info:eu-repo/semantics/other
oai:zenodo.org:3629594
2020-01-29T07:20:52Z
user-cami
openaire_data
Meyer, Fernando
2020-01-28
Genome binning of the gold standard pooled assembly. Refinement of the binning output of MaxBin 2.2.7, MetaBAT 2.12.1, CONCOCT 1.0.0, and DAS Tool 1.1.2.<br><strong>Software: </strong>DAS Tool<br><strong>SoftwareVersion: </strong>1.1.2<br><strong>DataURL: </strong> https://data.cami-challenge.org/participate<br><strong>SoftwareURL:</strong> https://github.com/cmks/DAS_Tool<br><strong>DockerImage:</strong> cami/das_tool:1.1.2<br><strong>IsBiobox:</strong> No<br><strong>ShortReadsUsed:</strong> True<br><strong>LongReadsUsed:</strong> False<br><strong>CommandUsed:</strong> DAS_Tool -i binning_concoct1.0.0,binning_maxbin2.2.7,binning_metabat2.12.1 -c anonymous_gsa_pooled.fasta -o output --search_engine diamond
https://doi.org/10.5281/zenodo.3629594
oai:zenodo.org:3629594
Zenodo
https://zenodo.org/communities/cami
https://doi.org/10.5281/zenodo.3629593
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
metagenomics
genome binning
CAMI 2 Mouse Gut Toy data set
DAS Tool 1.1.2 genome binning of the CAMI 2 Mouse Gut Toy data set, samples 0-63, gold standard pooled assembly
info:eu-repo/semantics/other
oai:zenodo.org:10560804
2024-01-25T07:54:59Z
user-cami
openaire
user-nfdi4microbiota
Fritz, Adrian
McHardy, Alice
2023-04-16
<p>Poster presented by Adrian Fritz on the 27th Annual International Conference on Research in Computational Molecular Biology April 16 -29 2023 in Istanbul. </p>
<div>
<p><strong><span>Abstract. </span></strong><span>A lot of progress has been made in the field of metagenomics in the past couple of years, both in terms of computational methods as well as in experimental setup and sequencing technologies. Still, new laboratory protocols, sequencing chemistries and metagenomics software are being developed and published all the time. Thus, it is important for the community to keep being able to assess and compare all these different methods. For this, being able to easily and quickly simulate metagenomic datasets is key.</span></p>
<p><span>The first version of CAMISIM was published in 2019 and was widely adopted as a simulation software for microbial communities and metagenomes. It provided the benchmark datasets for the first and second CAMI challenges as well as datasets for dozens of other software methods. To keep up with the current developments, CAMISIM is under constant development and received multiple updates and new releases since 2019. Now, we present the 2.0 version of CAMISIM, which not only brings CAMISIM up to speed with the latest recommendations for software workflows from different initiatives, but also solves some longer standing issues, includes the latest sequencing simulators and offers more customisation and flexibility to the users, while an extension from only metagenomics to also metatranscriptomics datasets is on the horizon.</span></p>
<p><span>All versions of CAMISIM are freely available under the Apache 2.0 license under https://github.com/CAMI-challenge/CAMISIM</span></p>
</div>
https://doi.org/10.5281/zenodo.10560804
oai:zenodo.org:10560804
Zenodo
https://zenodo.org/communities/cami
https://zenodo.org/communities/nfdi4microbiota
https://doi.org/10.5281/zenodo.10560803
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
RECOMB, 27th Annual International Conference on Research in Computational Molecular Biology, Istanbul, 16 - 19 April 2023
CAMISIM 2.0 – Simulating metagenomes and microbial communities
info:eu-repo/semantics/conferencePoster
oai:zenodo.org:3629626
2020-01-29T07:20:52Z
user-cami
openaire_data
Meyer, Fernando
2020-01-28
<strong>Software: </strong>mOTUs<br><strong>SoftwareVersion: </strong>2.5.1<br><strong>DataURL: </strong> https://data.cami-challenge.org/participate<br><strong>SoftwareURL:</strong> https://motu-tool.org/<br><strong>DockerImage:</strong> cami/motus:2.5.1<br><strong>IsBiobox:</strong> False<br><strong>ReferenceDatabase:</strong> mOTUs database version 2.5.0<br><strong>ShortReadsUsed:</strong> True<br><strong>LongReadsUsed:</strong> False<br><strong>CommandsUsed:</strong> for i in {0..63}; do motus profile -f sample_$((i))/reads/anonymous_reads_r1.fq -r sample_$((i))/reads/anonymous_reads_r2.fq -n $((i)) -C precision > sample$((i)).profile ; done<br>cat sample*.profile > cami2_mouse_gut_motus2.5.1.profile
https://doi.org/10.5281/zenodo.3629626
oai:zenodo.org:3629626
Zenodo
https://zenodo.org/communities/cami
https://doi.org/10.5281/zenodo.3629625
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
metagenomics
taxonomic profiling
CAMI 2 Mouse Gut Toy data set
mOTUs 2.5.1 taxonomic profiling of the CAMI 2 Mouse Gut Toy data set, samples 0-63
info:eu-repo/semantics/other
oai:zenodo.org:3664090
2020-02-12T19:21:06Z
user-cami
openaire_data
Lesker, Till Robin
2020-02-12
<p>Assembly of the first 10 short read samples<br>
<strong>Software: </strong>metaSPAdes<br>
<strong>SoftwareVersion: </strong>3.13.0<br>
<strong>DataURL: </strong> https://data.cami-challenge.org/participate<br>
<strong>SoftwareURL:</strong> https://github.com/ablab/spades<br>
<strong>ShortReadsUsed:</strong> True<br>
<strong>LongReadsUsed:</strong> False<br>
<strong>CommandUsed:</strong> conda create -n spades3130 spades=3.13.0-0<br>
<br>
Sample0=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_0/reads/anonymous_reads.fq.gz<br>
Sample1=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_1/reads/anonymous_reads.fq.gz<br>
Sample2=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_2/reads/anonymous_reads.fq.gz<br>
Sample3=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_3/reads/anonymous_reads.fq.gz<br>
Sample4=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_4/reads/anonymous_reads.fq.gz<br>
Sample5=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_5/reads/anonymous_reads.fq.gz<br>
Sample6=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_6/reads/anonymous_reads.fq.gz<br>
Sample7=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_7/reads/anonymous_reads.fq.gz<br>
Sample8=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_8/reads/anonymous_reads.fq.gz<br>
Sample9=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_9/reads/anonymous_reads.fq.gz<br>
<br>
cat $Sample0 $Sample1 $Sample2 $Sample3 $Sample4 $Sample5 $Sample6 $Sample7 $Sample8 $Sample9 > Samples0-9_anonymous_reads.fq.gz<br>
<br>
conda activate spades3130<br>
/usr/bin/time -v metaspades.py --12 Samples0-9_anonymous_reads.fq.gz -o metaSPAdes3130-Sample0-9</p>
https://doi.org/10.5281/zenodo.3664090
oai:zenodo.org:3664090
Zenodo
https://zenodo.org/communities/cami
https://doi.org/10.5281/zenodo.3664089
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
metagenomics
assembly
CAMI 2 Mouse Gut Toy data set
metaSPAdes 3.13.0 assembly of the CAMI 2 Mouse Gut Toy data set, samples 0-9, short reads
info:eu-repo/semantics/other
oai:zenodo.org:3629610
2020-01-29T07:20:52Z
user-cami
openaire_data
Meyer, Fernando
2020-01-28
<strong>Software: </strong>MetaPhlAn<br><strong>SoftwareVersion: </strong>2.9.21<br><strong>DataURL: </strong> https://data.cami-challenge.org/participate<br><strong>SoftwareURL:</strong> https://bitbucket.org/biobakery/metaphlan2<br><strong>DockerImage:</strong> cami/metaphlan:2.9.21<br><strong>IsBiobox:</strong> True<br><strong>BioboxYAMLFile:</strong> https://zenodo.org/record/3629567/files/biobox.yaml?download=1<br><strong>ReferenceDatabase:</strong> mpa_v29_CHOCOPhlAn_201901 <br><strong>ShortReadsUsed:</strong> True<br><strong>LongReadsUsed:</strong> False<br><strong>CommandsUsed:</strong> docker run \<br>--volume="/path/to/19122017_mousegut_scaffolds_yaml:/bbx/mnt/yaml:ro" \<br>--volume="/path/to/19122017_mousegut_scaffolds:/bbx/mnt/input:ro" \<br>--volume="/path/to/output:/bbx/mnt/output:rw" \<br>--volume="/path/to/output/metadata:/bbx/metadata:rw" \<br>--volume="/path/to/output/cache:/cache:rw" \<br>--volume="/path/to/reference_database:/exchange/db:rw" \<br>cami/metaphlan:2.9.21
https://doi.org/10.5281/zenodo.3629610
oai:zenodo.org:3629610
Zenodo
https://zenodo.org/communities/cami
https://doi.org/10.5281/zenodo.3629609
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
metagenomics
taxonomic profiling
CAMI 2 Mouse Gut Toy data set
MetaPhlAn 2.9.21 taxonomic profiling of the CAMI 2 Mouse Gut Toy data set, samples 0-63
info:eu-repo/semantics/other
oai:zenodo.org:3629632
2020-01-29T07:20:52Z
user-cami
openaire_data
Meyer, Fernando
2020-01-28
<strong>Software: </strong>MetaPhyler<br><strong>SoftwareVersion: </strong>1.25<br><strong>DataURL: </strong> https://data.cami-challenge.org/participate<br><strong>SoftwareURL:</strong> http://metaphyler.cbcb.umd.edu/<br><strong>DockerImage:</strong> stefanjanssen/docker_profiling_tools:metaphyler<br><strong>IsBiobox:</strong> True<br><strong>BioboxYAMLFile:</strong> https://zenodo.org/record/3629567/files/biobox.yaml?download=1<br><strong>ReferenceDatabase:</strong> 2012<br><strong>ShortReadsUsed:</strong> True<br><strong>LongReadsUsed:</strong> False<br><strong>CommandsUsed:</strong> docker run \<br>--volume="/path/to/19122017_mousegut_scaffolds_yaml:/bbx/mnt/yaml:ro" \<br>--volume="/path/to/19122017_mousegut_scaffolds:/bbx/mnt/input:ro" \<br>--volume="/path/to/output:/bbx/mnt/output:rw" \<br>--volume="/path/to/output/metadata:/bbx/metadata:rw" \<br>--volume="/path/to/output/cache:/cache:rw" \<br>stefanjanssen/docker_profiling_tools:metaphyler
https://doi.org/10.5281/zenodo.3629632
oai:zenodo.org:3629632
Zenodo
https://zenodo.org/communities/cami
https://doi.org/10.5281/zenodo.3629631
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
metagenomics
taxonomic profiling
CAMI 2 Mouse Gut Toy data set
MetaPhyler 1.25 taxonomic profiling of the CAMI 2 Mouse Gut Toy data set, samples 0-63
info:eu-repo/semantics/other
oai:zenodo.org:3629620
2020-01-29T07:20:52Z
user-cami
openaire_data
Meyer, Fernando
2020-01-28
<strong>Software: </strong>FOCUS<br><strong>SoftwareVersion: </strong>0.31<br><strong>DataURL: </strong> https://data.cami-challenge.org/participate<br><strong>SoftwareURL:</strong> https://github.com/metageni/FOCUS<br><strong>DockerImage:</strong> stefanjanssen/docker_profiling_tools:focus<br><strong>IsBiobox:</strong> True<br><strong>BioboxYAMLFile:</strong> https://zenodo.org/record/3629567/files/biobox.yaml?download=1<br><strong>ReferenceDatabase:</strong> k8_bacterial_and_draft<br><strong>ShortReadsUsed:</strong> True<br><strong>LongReadsUsed:</strong> False<br><strong>CommandsUsed:</strong> docker run \<br>--volume="/path/to/19122017_mousegut_scaffolds_yaml:/bbx/mnt/yaml:ro" \<br>--volume="/path/to/19122017_mousegut_scaffolds:/bbx/mnt/input:ro" \<br>--volume="/path/to/output:/bbx/mnt/output:rw" \<br>--volume="/path/to/output/metadata:/bbx/metadata:rw" \<br>--volume="/path/to/output/cache:/cache:rw" \<br>stefanjanssen/docker_profiling_tools:focus
https://doi.org/10.5281/zenodo.3629620
oai:zenodo.org:3629620
Zenodo
https://zenodo.org/communities/cami
https://doi.org/10.5281/zenodo.3629619
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
metagenomics
taxonomic profiling
CAMI 2 Mouse Gut Toy data set
FOCUS 0.31 taxonomic profiling of the CAMI 2 Mouse Gut Toy data set, samples 0-63
info:eu-repo/semantics/other
oai:zenodo.org:3629612
2020-01-29T07:20:52Z
user-cami
openaire_data
Meyer, Fernando
2020-01-28
<strong>Software: </strong>MetaPhlAn<br><strong>SoftwareVersion: </strong>2.2.0<br><strong>DataURL: </strong> https://data.cami-challenge.org/participate<br><strong>SoftwareURL:</strong> https://bitbucket.org/biobakery/metaphlan2<br><strong>DockerImage:</strong> stefanjanssen/docker_profiling_tools:metaphlan2<br><strong>IsBiobox:</strong> True<br><strong>BioboxYAMLFile:</strong> https://zenodo.org/record/3629567/files/biobox.yaml?download=1<br><strong>ReferenceDatabase:</strong> mpa_v20_m200<br><strong>ShortReadsUsed:</strong> True<br><strong>LongReadsUsed:</strong> False<br><strong>CommandsUsed:</strong> docker run \<br>--volume="/path/to/19122017_mousegut_scaffolds_yaml:/bbx/mnt/yaml:ro" \<br>--volume="/path/to/19122017_mousegut_scaffolds:/bbx/mnt/input:ro" \<br>--volume="/path/to/output:/bbx/mnt/output:rw" \<br>--volume="/path/to/output/metadata:/bbx/metadata:rw" \<br>--volume="/path/to/output/cache:/cache:rw" \<br>stefanjanssen/docker_profiling_tools:metaphlan2
https://doi.org/10.5281/zenodo.3629612
oai:zenodo.org:3629612
Zenodo
https://zenodo.org/communities/cami
https://doi.org/10.5281/zenodo.3629611
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
metagenomics
taxonomic profiling
CAMI 2 Mouse Gut Toy data set
MetaPhlAn 2.2.0 taxonomic profiling of the CAMI 2 Mouse Gut Toy data set, samples 0-63
info:eu-repo/semantics/other
oai:zenodo.org:3629622
2020-01-29T07:20:52Z
user-cami
openaire_data
Meyer, Fernando
2020-01-28
<strong>Software: </strong>CAMIARKQuikr<br><strong>SoftwareVersion: </strong>1.0.0<br><strong>DataURL: </strong> https://data.cami-challenge.org/participate<br><strong>SoftwareURL:</strong> https://doi.org/10.5281/zenodo.1730572<br><strong>DockerImage:</strong> stefanjanssen/docker_profiling_tools:quickr<br><strong>IsBiobox:</strong> True<br><strong>BioboxYAMLFile:</strong> https://zenodo.org/record/3629567/files/biobox.yaml?download=1<br><strong>ReferenceDatabase:</strong> https://doi.org/10.5281/zenodo.1730572<br><strong>ShortReadsUsed:</strong> True<br><strong>LongReadsUsed:</strong> False<br><strong>CommandsUsed:</strong> docker run \<br>--volume="/path/to/19122017_mousegut_scaffolds_yaml:/bbx/mnt/yaml:ro" \<br>--volume="/path/to/19122017_mousegut_scaffolds:/bbx/mnt/input:ro" \<br>--volume="/path/to/output:/bbx/mnt/output:rw" \<br>--volume="/path/to/output/metadata:/bbx/metadata:rw" \<br>--volume="/path/to/output/cache:/cache:rw" \<br>stefanjanssen/docker_profiling_tools:quickr
https://doi.org/10.5281/zenodo.3629622
oai:zenodo.org:3629622
Zenodo
https://zenodo.org/communities/cami
https://doi.org/10.5281/zenodo.3629621
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
metagenomics
taxonomic profiling
CAMI 2 Mouse Gut Toy data set
CAMIARKQuikr 1.0.0 taxonomic profiling of the CAMI 2 Mouse Gut Toy data set, samples 0-63
info:eu-repo/semantics/other
oai:zenodo.org:3629602
2020-01-29T07:20:52Z
user-cami
openaire_data
Meyer, Fernando
2020-01-28
<p>Taxonomic binning of the gold standard pooled assembly<br>
<strong>Software: </strong>PhyloPythiaS+<br>
<strong>SoftwareVersion: </strong>1.4<br>
<strong>DataURL: </strong> https://data.cami-challenge.org/participate<br>
<strong>SoftwareURL:</strong> https://github.com/algbioi/ppsp<br>
<strong>DockerImage:</strong> cami/ppsp:1.4<br>
<strong>IsBiobox:</strong> False<br>
<strong>ReferenceDatabase:</strong> RefSeq 93, SILVA 132<br>
<strong>Taxonomy:</strong> NCBI 2018-02-26<br>
<strong>ShortReadsUsed:</strong> False<br>
<strong>LongReadsUsed:</strong> False<br>
<strong>CommandUsed:</strong> run_ppsp.py --pipelineDir ppsp_pipepline --inputFastaFile anonymous_gsa_pooled.fasta --databaseFile ncbi_taxonomy --refSeq refseq93 --s16Database SILVA_132 --mgDatabase reference_NCBI201502/mg5</p>
https://doi.org/10.5281/zenodo.3629602
oai:zenodo.org:3629602
Zenodo
https://zenodo.org/communities/cami
https://doi.org/10.5281/zenodo.3629601
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
metagenomics
taxonomic binning
CAMI 2 Mouse Gut Toy data set
PhyloPythiaS+ 1.4 taxonomic binning of the CAMI 2 Mouse Gut Toy data set, gold standard pooled assembly
info:eu-repo/semantics/other
oai:zenodo.org:3629606
2020-01-29T07:20:52Z
user-cami
openaire_data
Meyer, Fernando
2020-01-28
<p>Taxonomic binning of the gold standard pooled assembly<br>
<strong>Software: </strong>MEGAN<br>
<strong>SoftwareVersion: </strong>6.15.2<br>
<strong>DataURL: </strong> https://data.cami-challenge.org/participate<br>
<strong>SoftwareURL:</strong> https://github.com/husonlab/megan-ce<br>
<strong>ReferenceDatabase:</strong> NCBI nr 2019-04-17<br>
<strong>Taxonomy:</strong> NCBI 2019-04-17<br>
<strong>ShortReadsUsed:</strong> False<br>
<strong>LongReadsUsed:</strong> False<br>
<strong>CommandUsed:</strong> diamond makedb --in nr.faa.gz --db nr_diamond0.9.24 --taxonmap prot.accession2taxid.gz --taxonnodes nodes.dmp<br>
diamond blastx -d nr_diamond0.9.24 -q anonymous_gsa_pooled.fasta -a result -t tmp --index-chunks 1<br>
megan/tools/daa2rma -i result.daa -o 19122017_mousegut_scaffolds.rma --acc2taxa megan/prot_acc2tax-Nov2018X1.abin<br>
#final bins extracted with MEGAN's graphical interface tool</p>
https://doi.org/10.5281/zenodo.3629606
oai:zenodo.org:3629606
Zenodo
https://zenodo.org/communities/cami
https://doi.org/10.5281/zenodo.3629605
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
metagenomics
taxonomic binning
CAMI 2 Mouse Gut Toy data set
MEGAN 6.15.2 taxonomic binning of the CAMI 2 Mouse Gut Toy data set, gold standard pooled assembly
info:eu-repo/semantics/other
oai:zenodo.org:3629624
2020-01-29T07:20:52Z
user-cami
openaire_data
Meyer, Fernando
2020-01-28
<strong>Software: </strong>mOTUs<br><strong>SoftwareVersion: </strong>1.1<br><strong>DataURL: </strong> https://data.cami-challenge.org/participate<br><strong>SoftwareURL:</strong> http://www.bork.embl.de/software/mOTUs1/<br><strong>DockerImage:</strong> stefanjanssen/docker_profiling_tools:motu<br><strong>IsBiobox:</strong> True<br><strong>BioboxYAMLFile:</strong> https://zenodo.org/record/3629567/files/biobox.yaml?download=1<br><strong>ReferenceDatabase:</strong> mOTU.v1.padded<br><strong>ShortReadsUsed:</strong> True<br><strong>LongReadsUsed:</strong> False<br><strong>CommandsUsed:</strong> docker run \<br>--volume="/path/to/19122017_mousegut_scaffolds_yaml:/bbx/mnt/yaml:ro" \<br>--volume="/path/to/19122017_mousegut_scaffolds:/bbx/mnt/input:ro" \<br>--volume="/path/to/output:/bbx/mnt/output:rw" \<br>--volume="/path/to/output/metadata:/bbx/metadata:rw" \<br>--volume="/path/to/output/cache:/cache:rw" \<br>stefanjanssen/docker_profiling_tools:motu
https://doi.org/10.5281/zenodo.3629624
oai:zenodo.org:3629624
Zenodo
https://zenodo.org/communities/cami
https://doi.org/10.5281/zenodo.3629623
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
metagenomics
taxonomic profiling
CAMI 2 Mouse Gut Toy data set
mOTUs 1.1 taxonomic profiling of the CAMI 2 Mouse Gut Toy data set, samples 0-63
info:eu-repo/semantics/other
oai:zenodo.org:3632528
2020-01-31T19:20:51Z
user-cami
openaire_data
Meyer, Fernando
2020-01-31
<p><strong>DataURL: </strong> https://data.cami-challenge.org/participate</p>
https://doi.org/10.5281/zenodo.3632528
oai:zenodo.org:3632528
Zenodo
https://zenodo.org/communities/cami
https://doi.org/10.5281/zenodo.3632527
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
metagenomics
taxonomic profiling
CAMI 2 Mouse Gut Toy data set
Gold standard taxonomic profile of the CAMI 2 Mouse Gut Toy data set, samples 0-63
info:eu-repo/semantics/other
oai:zenodo.org:3663885
2020-02-12T19:21:06Z
user-cami
openaire_data
Lesker, Till Robin
2020-02-12
<p>Assembly of the first 10 short read samples with different MEGAHIT versions and parameters<br>
<strong>Software: </strong>MEGAHIT<br>
<strong>SoftwareVersion: </strong>1.0.3, 1.1.3, 1.2.9<br>
<strong>DataURL: </strong> https://data.cami-challenge.org/participate<br>
<strong>SoftwareURL:</strong> https://github.com/voutcn/megahit<br>
<strong>ShortReadsUsed:</strong> True<br>
<strong>LongReadsUsed:</strong> False<br>
<strong>CommandUsed:</strong> # install bioconda and run:<br>
conda create -n megahit103 megahit=1.0.3<br>
conda create -n megahit113 megahit=1.1.3<br>
conda create -n megahit129 megahit=1.2.9<br>
<br>
Sample0=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_0/reads/anonymous_reads.fq.gz<br>
Sample1=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_1/reads/anonymous_reads.fq.gz<br>
Sample2=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_2/reads/anonymous_reads.fq.gz<br>
Sample3=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_3/reads/anonymous_reads.fq.gz<br>
Sample4=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_4/reads/anonymous_reads.fq.gz<br>
Sample5=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_5/reads/anonymous_reads.fq.gz<br>
Sample6=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_6/reads/anonymous_reads.fq.gz<br>
Sample7=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_7/reads/anonymous_reads.fq.gz<br>
Sample8=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_8/reads/anonymous_reads.fq.gz<br>
Sample9=/path/to/19122017_mousegut_scaffolds/2017.12.29_11.37.26_sample_9/reads/anonymous_reads.fq.gz<br>
<br>
conda activate megahit103<br>
/usr/bin/time -v megahit -t 48 \<br>
--12 $Sample0 --12 $Sample1 --12 $Sample2 --12 $Sample3 --12 $Sample4 --12 $Sample5 --12 $Sample6 --12 $Sample7 --12 $Sample8 --12 $Sample9 \<br>
-o megahit103-Sample0-9-sLibs-default<br>
<br>
conda activate megahit113<br>
/usr/bin/time -v megahit -t 48 \<br>
--12 $Sample0 --12 $Sample1 --12 $Sample2 --12 $Sample3 --12 $Sample4 --12 $Sample5 --12 $Sample6 --12 $Sample7 --12 $Sample8 --12 $Sample9 \<br>
-o megahit113-Sample0-9-sLibs-default<br>
<br>
/usr/bin/time -v megahit -t 48 --presets meta-sensitive \<br>
--12 $Sample0 --12 $Sample1 --12 $Sample2 --12 $Sample3 --12 $Sample4 --12 $Sample5 --12 $Sample6 --12 $Sample7 --12 $Sample8 --12 $Sample9 \<br>
-o megahit113-Sample0-9-sLibs-meta-sensitive<br>
<br>
/usr/bin/time -v megahit -t 48 --presets meta-large \<br>
--12 $Sample0 --12 $Sample1 --12 $Sample2 --12 $Sample3 --12 $Sample4 --12 $Sample5 --12 $Sample6 --12 $Sample7 --12 $Sample8 --12 $Sample9 \<br>
-o megahit113-Sample0-9-sLibs-meta-large<br>
<br>
conda activate megahit129<br>
/usr/bin/time -v megahit -t 48 \<br>
--12 $Sample0 --12 $Sample1 --12 $Sample2 --12 $Sample3 --12 $Sample4 --12 $Sample5 --12 $Sample6 --12 $Sample7 --12 $Sample8 --12 $Sample9 \<br>
-o megahit129-Sample0-9-sLibs-default</p>
https://doi.org/10.5281/zenodo.3663885
oai:zenodo.org:3663885
Zenodo
https://zenodo.org/communities/cami
https://doi.org/10.5281/zenodo.3663884
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
metagenomics
assembly
CAMI 2 Mouse Gut Toy data set
MEGAHIT 1.0.3, 1.1.3, 1.2.9 assembly of the CAMI 2 Mouse Gut Toy data set, samples 0-9, short reads
info:eu-repo/semantics/other
oai:zenodo.org:3629598
2020-01-29T07:20:52Z
user-cami
openaire_data
Meyer, Fernando
2020-01-28
<p>Taxonomic binning of the gold standard pooled assembly<br>
<strong>Software: </strong>DIAMOND<br>
<strong>SoftwareVersion: </strong>0.9.24<br>
<strong>DataURL: </strong> https://data.cami-challenge.org/participate<br>
<strong>SoftwareURL:</strong> https://github.com/bbuchfink/diamond<br>
<strong>ReferenceDatabase:</strong> NCBI nr 2019-04-17<br>
<strong>Taxonomy:</strong> NCBI 2019-04-17<br>
<strong>ShortReadsUsed:</strong> False<br>
<strong>LongReadsUsed:</strong> False<br>
<strong>CommandUsed:</strong> diamond makedb --in nr.faa.gz --db nr --taxonmap prot.accession2taxid.gz --taxonnodes nodes.dmp<br>
diamond blastx --query anonymous_gsa_pooled.fasta --db nr --outfmt 102 --out 19122017_mousegut_scaffolds.out --block-size 40 --index-chunks 1 --tmpdir tmp</p>
https://doi.org/10.5281/zenodo.3629598
oai:zenodo.org:3629598
Zenodo
https://zenodo.org/communities/cami
https://doi.org/10.5281/zenodo.3629597
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
metagenomics
taxonomic binning
CAMI 2 Mouse Gut Toy data set
DIAMOND 0.9.24 taxonomic binning of the CAMI 2 Mouse Gut Toy data set, gold standard pooled assembly
info:eu-repo/semantics/other
oai:zenodo.org:3632511
2020-01-31T19:20:51Z
user-cami
openaire_data
Meyer, Fernando
2020-01-31
<p>Gold standard genome and taxonomic binning of the CAMI 2 Mouse Gut Toy data set, gold standard pooled assembly<br>
<strong>DataURL: </strong> https://data.cami-challenge.org/participate</p>
https://doi.org/10.5281/zenodo.3632511
oai:zenodo.org:3632511
Zenodo
https://zenodo.org/communities/cami
https://doi.org/10.5281/zenodo.3632510
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
metagenomics
genome binning
taxonomic binning
CAMI 2 Mouse Gut Toy data set
Gold standard genome and taxonomic binning of the CAMI 2 Mouse Gut Toy data set, gold standard pooled assembly
info:eu-repo/semantics/other
oai:zenodo.org:3667475
2020-02-15T07:20:50Z
user-cami
openaire_data
Meyer, Fernando
2020-02-14
<p>Genome coverage (short reads) averaged over the 64 samples of the CAMI 2 Mouse Gut Toy data set</p>
https://doi.org/10.5281/zenodo.3667475
oai:zenodo.org:3667475
Zenodo
https://zenodo.org/communities/cami
https://doi.org/10.5281/zenodo.3667474
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
metagenomics
CAMI 2 Mouse Gut Toy data set
Average genome coverage of the CAMI 2 Mouse Gut Toy data set
info:eu-repo/semantics/other
oai:zenodo.org:10728291
2024-03-01T06:33:38Z
user-cami
openaire
user-nfdi4microbiota
Meyer, Fernando
Fritz, Adrian
McHardy, Alice C.
2023-07-23
<p>Poster presented by Fernando Meyer at the 31st Conference on Intelligent Systems for Molecular Biology and 22nd European Conference on Computational Biology, July 23-27, 2023, in Lyon, France.</p>
<p>Metagenome interpretation depends on the recovery of high-quality genomes from short-read data through the application of performant assemblers followed by binners. The Initiative for the Critical Assessment of Metagenome Interpretation (CAMI) analyzed the results of a large number of methods thoroughly on benchmark datasets. Several binners in the CAMI II challenges performed well on gold standards representing perfect assemblies. However, performance was impacted on assemblies of MEGAHIT. To investigate whether certain methods are particularly capable of recovering high-quality genomes, here we benchmark various combinations of assemblers and binners on the marine dataset of the CAMI II challenge.</p>
https://doi.org/10.5281/zenodo.10728291
oai:zenodo.org:10728291
Zenodo
https://zenodo.org/communities/cami
https://zenodo.org/communities/nfdi4microbiota
https://doi.org/10.5281/zenodo.10728290
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
ISMB/ECCB, 31st Conference on Intelligent Systems for Molecular Biology and 22nd European Conference on Computational Biology, Lyon, France, July 23-27, 2023
Assessing metagenome recovery from combinations of assemblers and binners
info:eu-repo/semantics/conferencePoster
oai:zenodo.org:3629600
2020-01-29T07:20:52Z
user-cami
openaire_data
Meyer, Fernando
2020-01-28
<p>Taxonomic binning of the gold standard pooled assembly<br>
<strong>Software: </strong>Kraken<br>
<strong>SoftwareVersion: </strong>2.0.8 beta<br>
<strong>DataURL: </strong> https://data.cami-challenge.org/participate<br>
<strong>SoftwareURL:</strong> https://ccb.jhu.edu/software/kraken2/<br>
<strong>ReferenceDatabase:</strong> built 2019-05-22<br>
<strong>Taxonomy:</strong> NCBI 2019-05-22<br>
<strong>ShortReadsUsed:</strong> False<br>
<strong>LongReadsUsed:</strong> False<br>
<strong>CommandUsed:</strong> kraken2-build --standard --db kraken2db_std --use-ftp<br>
kraken2 --db kraken2db_std --threads 16 --output 19122017_mousegut_scaffolds.kraken --report 19122017_mousegut_scaffolds.kreport anonymous_gsa_pooled.fasta<br>
cat 19122017_mousegut_scaffolds | awk '{print $2 "\t" $3}' > 19122017_mousegut_scaffolds.cami</p>
https://doi.org/10.5281/zenodo.3629600
oai:zenodo.org:3629600
Zenodo
https://zenodo.org/communities/cami
https://doi.org/10.5281/zenodo.3629599
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
metagenomics
taxonomic binning
CAMI 2 Mouse Gut Toy data set
Kraken 2.0.8 beta taxonomic binning of the CAMI 2 Mouse Gut Toy data set, gold standard pooled assembly
info:eu-repo/semantics/other
oai:zenodo.org:5013479
2022-01-07T13:37:35Z
user-cami
openaire_data
Fritz, Adrian
2021-06-22
<p>Assembly submissions, including participants' submissions, of the CAMI 2 challenge data sets.</p>
<p>The gold standards can be found either on the CAMI 2 challenge website: <a href="https://data.cami-challenge.org/participate">https://data.cami-challenge.org/participate</a> or in publisso alongside the data sets: https://repository.publisso.de/resource/frl:6425521</p>
<p>Also see <a href="https://www.microbiome-cosi.org/cami">https://www.microbiome-cosi.org/cami</a> </p>
https://doi.org/10.5281/zenodo.5013479
oai:zenodo.org:5013479
eng
Zenodo
https://zenodo.org/communities/cami
https://doi.org/10.5281/zenodo.5013478
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Assemblies of the CAMI 2 challenge data sets
info:eu-repo/semantics/other