linsalrob/ComputationalGenomicsManual-v2.zip
linsalrob-ComputationalGenomicsManual-d2e7498
.gitattributes
43 Bytes
.gitignore
1.3 kB
16S
16S.pdf
1.1 MB
README.md
16.7 kB
images
16Sgraph.png
114.0 kB
banner.png
7.1 kB
calypso_data_summary.png
78.6 kB
calypso_start.png
10.8 kB
copyrighter.png
116.4 kB
dada_provenance.png
12.7 kB
data_filtering.png
68.9 kB
filter_normalize.png
2.4 kB
next.png
1.3 kB
normalization_tfm.png
89.8 kB
rep_seqs.png
161.3 kB
seq_tree.png
191.1 kB
successful_normalize.png
5.0 kB
successful_parse.png
7.0 kB
successful_parsed_counts.png
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successful_qiime.png
5.9 kB
table_summary.png
45.2 kB
upload_optional_files.png
60.6 kB
upload_own_data.png
86.8 kB
ANVIO
ANVIO.pdf
36.1 kB
README.md
6.7 kB
images
aws_rules.png
35.9 kB
inbound.png
71.8 kB
outbound.png
49.6 kB
security.md
2.2 kB
security.pdf
129.4 kB
AnnotationPipelines
AnnotationPipelines.pdf
168.4 kB
README.md
5.1 kB
images
new_folder.png
2.7 kB
rast_chooser.png
5.1 kB
rast_job_info.png
42.1 kB
rast_pipeline.png
89.6 kB
rast_summ_stats.png
25.9 kB
AntibioticResistance
images
resistance.png
204.0 kB
Assignments
Assignments.pdf
12.6 kB
GenomicsAssignment
README.md
5.2 kB
klebsiella.txt
3.2 kB
MetagenomicsAssignment
README.md
8.3 kB
NCBIEDirectAssignment
README.md
1.2 kB
genera.txt
1.7 kB
README.md
840 Bytes
CheckM
CheckM.pdf
18.9 kB
README.md
2.7 kB
images
checkm.png
47.7 kB
Conda
README.md
4.5 kB
CrossAssembly
CCOM.md
1.8 kB
CCOM.pdf
17.1 kB
CrossAssembly.pdf
54.6 kB
Metabat.md
2.4 kB
Metabat.pdf
18.6 kB
README.md
22.0 kB
images
CCOM.png
192.5 kB
metabat.png
84.1 kB
nineteencontigs.png
50.3 kB
spades.png
3.3 kB
Databases
Databases.pdf
38.4 kB
NCBI_Edirect.md
11.2 kB
NCBI_Edirect.pdf
38.6 kB
README.md
14.3 kB
SRA.md
17.7 kB
SRA.pdf
210.7 kB
SRA_WGS_Abstracts.tsv
2.8 MB
images
1772048.png
89.1 kB
DDBJ.png
2.9 kB
EMBL.png
9.6 kB
GenBankGrowth.png
62.8 kB
GroundwaterSize.png
19.9 kB
JGI.jpg
62.3 kB
JGI.png
25.1 kB
Mappers.png
82.8 kB
NCBI.png
4.8 kB
NCBIEDirect.png
10.4 kB
TARASize.png
7.9 kB
UniProt.png
10.0 kB
groundwater.png
93.5 kB
kegg.png
13.6 kB
pdb.png
33.0 kB
seed.png
32.3 kB
Datasets
.gitattributes
128 Bytes
CF
788707_20171213_S_R1.fastq.gz
133 Bytes
788707_20171213_S_R2.fastq.gz
133 Bytes
788707_20180129_S_R1.fastq.gz
133 Bytes
788707_20180129_S_R2.fastq.gz
133 Bytes
788707_20180313_S_R1.fastq.gz
133 Bytes
788707_20180313_S_R2.fastq.gz
133 Bytes
788707_20181126_S_R1.fastq.gz
133 Bytes
788707_20181126_S_R2.fastq.gz
133 Bytes
README.md
126 Bytes
Datasets.pdf
15.1 kB
README.md
1.8 kB
coral_algae
Algae.tgz
133 Bytes
CCA.tgz
133 Bytes
Control.tgz
133 Bytes
Coral.tgz
133 Bytes
README.md
3.6 kB
fastq
Algae_11.fastq.gz
133 Bytes
Algae_12.fastq.gz
133 Bytes
Algae_13.fastq.gz
133 Bytes
Algae_14.fastq.gz
132 Bytes
CCA_11.fastq.gz
133 Bytes
CCA_12.fastq.gz
132 Bytes
CCA_13.fastq.gz
133 Bytes
Control_11.fastq.gz
133 Bytes
Control_12.fastq.gz
133 Bytes
Control_13.fastq.gz
132 Bytes
Control_14.fastq.gz
133 Bytes
Coral_11.fastq.gz
133 Bytes
Coral_12.fastq.gz
133 Bytes
Coral_13.fastq.gz
132 Bytes
Coral_14.fastq.gz
133 Bytes
drinking_water
Calypso
README.md
163 Bytes
feature-table.biom
33.8 kB
metadata_calypso.tsv
1.2 kB
taxonomy.tsv
3.9 kB
README.md
3.5 kB
fastq
barcodes.fastq.gz
132 Bytes
sequences.fastq.gz
133 Bytes
metadata.tsv
1.1 kB
ground_water
README.md
3.7 kB
fastq
SRR3546449_pass_1.fastq.gz
131 Bytes
SRR3546449_pass_2.fastq.gz
131 Bytes
SRR3546450_pass_1.fastq.gz
131 Bytes
SRR3546450_pass_2.fastq.gz
131 Bytes
SRR3546451_pass_1.fastq.gz
131 Bytes
SRR3546451_pass_2.fastq.gz
131 Bytes
SRR3546452_pass_1.fastq.gz
131 Bytes
SRR3546452_pass_2.fastq.gz
131 Bytes
SRR3546453_pass_1.fastq.gz
131 Bytes
SRR3546453_pass_2.fastq.gz
131 Bytes
SRR3546454_pass_1.fastq.gz
131 Bytes
SRR3546454_pass_2.fastq.gz
131 Bytes
SRR3546455_pass_1.fastq.gz
131 Bytes
SRR3546455_pass_2.fastq.gz
131 Bytes
SRR3546457_pass_1.fastq.gz
131 Bytes
SRR3546457_pass_2.fastq.gz
131 Bytes
gut
README.md
5.0 kB
fastq
SRR3466404_pass_1.fastq.gz
133 Bytes
SRR3466404_pass_2.fastq.gz
133 Bytes
SRR3506419_pass_1.fastq.gz
133 Bytes
SRR3506419_pass_2.fastq.gz
133 Bytes
SRR3506420_pass_1.fastq.gz
133 Bytes
SRR3506420_pass_2.fastq.gz
133 Bytes
SRR3546776_pass_1.fastq.gz
133 Bytes
SRR3546776_pass_2.fastq.gz
133 Bytes
SRR3546778_pass_1.fastq.gz
133 Bytes
SRR3546778_pass_2.fastq.gz
133 Bytes
SRR3546779_pass_1.fastq.gz
133 Bytes
SRR3546779_pass_2.fastq.gz
133 Bytes
SRR3546780_pass_1.fastq.gz
133 Bytes
SRR3546780_pass_2.fastq.gz
133 Bytes
SRR3546781_pass_1.fastq.gz
133 Bytes
SRR3546781_pass_2.fastq.gz
133 Bytes
SRR3546782_pass_1.fastq.gz
133 Bytes
SRR3546782_pass_2.fastq.gz
133 Bytes
Definitions.md
936 Bytes
FOCUS
FOCUS.pdf
20.9 kB
README.md
2.9 kB
images
focus.jpg
86.1 kB
GenomePeek
GenomePeek.pdf
17.2 kB
README.md
2.4 kB
images
metagenome.png
179.6 kB
mixed.png
45.7 kB
single.png
35.9 kB
GenomeSequencingOverview
GenomeSequencingOverview.pdf
335.7 kB
README.md
8.3 kB
Whole_Genome_Sequencing.pdf
468.7 kB
images
GenBankGrowth.png
35.5 kB
GenomesOnlineGrowth.png
38.7 kB
GenomicsAndModeling.png
271.5 kB
Kraken2
README.md
2.8 kB
LICENSE
1.1 kB
Linux
AWS_SAGC2021_Setup.sh
12.4 kB
AWS_Setup.txt
17.8 kB
Linux.pdf
428.6 kB
MachineSetUp.md
53 Bytes
MachineSetUp.pdf
5.5 kB
README.md
19.3 kB
images
image1.png
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image10.png
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image11.png
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image12.png
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image13.png
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image14.png
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image15.png
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image16.png
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image17.png
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image18.png
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image19.jpg
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image2.png
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image20.png
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image21.png
45.0 kB
image3.png
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image4.png
15.8 kB
image5.png
14.3 kB
image6.png
22.3 kB
image7.png
35.7 kB
image8.png
77.6 kB
image9.png
16.0 kB
mobaxterm_key.png
20.9 kB
mobaxterm_ssh.png
27.4 kB
MMSeqs2
README.md
4.8 kB
Metagenomics
AnnotatingOrfMSeed.md
2.9 kB
AnnotatingOrfMSeed.pdf
18.3 kB
ExampleDataSets.md
3.5 kB
ExampleDataSets.pdf
23.0 kB
Metagenomics.pdf
252.7 kB
README.md
19.9 kB
images
1ng vs 100ng.png
31.3 kB
BAC Cloning.png
139.6 kB
CDA.png
129.3 kB
CDA_Small.png
39.7 kB
Earth Microbiome Project.png
48.2 kB
Filters.png
54.8 kB
Findley_PCA.png
13.3 kB
Handelsman1.png
33.1 kB
Handelsman2.png
57.0 kB
RDP.png
9.3 kB
SSU_RNApol.png
131.0 kB
Silva.png
42.5 kB
Staley_Konopka.png
64.3 kB
Subsystems.png
33.5 kB
VAMPS.png
76.7 kB
Woese_Tree.png
245.5 kB
abrolhos.png
36.5 kB
acridine orange.png
188.2 kB
plate counts.png
50.4 kB
plate_count_anomaly.gif
102.6 kB
qiita.png
11.7 kB
who_what_where.png
22.6 kB
ORFCalling
ORFCalling.pdf
149.3 kB
README.md
10.8 kB
images
blastx.png
9.5 kB
transcription_translation.png
120.4 kB
PATRIC
GenomeSets.md
7.6 kB
GenomeSets.pdf
34.2 kB
PATRIC.pdf
18.7 kB
README.md
2.4 kB
Python
README.md
4.0 kB
Zen_of_python.md
1.0 kB
README.md
5.2 kB
RTMg
README.md
8.4 kB
RTMg.pdf
31.8 kB
images
sens.png
59.3 kB
References
README.md
17.9 kB
References.pdf
34.4 kB
RemovingContamination
README.md
9.2 kB
SUPER-FOCUS
README.md
1.2 kB
SUPER-FOCUS.pdf
107.9 kB
images
sf-logo.png
101.7 kB
SequenceAssembly
N50.md
1.1 kB
N50.pdf
14.9 kB
README.md
6.8 kB
SequenceAssembly.pdf
32.5 kB
images
reads_contigs_scaffolds.png
23.1 kB
SequenceFileFormats
INSDC_Features.md
9.1 kB
INSDC_Features.pdf
38.9 kB
README.md
19.2 kB
SequenceFileFormats.pdf
294.1 kB
images
ascii.png
100.3 kB
crAssphageDNA.png
17.6 kB
crAssphageQuality.png
32.7 kB
fastq.png
8.3 kB
prinseq.png
19.2 kB
SequenceQC
IlluminaAdapters.fa
1.1 kB
README.md
9.4 kB
SequenceQC.pdf
170.8 kB
images
BadLength.png
11.9 kB
GoodLength.png
12.1 kB
IonTorrentQual.gif
37.3 kB
Sequencing
README.md
24.0 kB
Sequencing.pdf
924.1 kB
images
GrowthSRA_SeqCost.png
105.4 kB
SangerCrassphage.png
97.6 kB
SangerCrassphageError.png
2.0 kB
image1.png
107.9 kB
image2.png
151.5 kB
image3.png
170.8 kB
image4.png
131.6 kB
image5.png
182.9 kB
image6.png
100.0 kB
sanger_seq.png
44.7 kB
tagmentation.png
160.1 kB
Snakemake
README.md
6.0 kB
fastp.snakefile
1.6 kB
filter_assemble.snakefile
2.3 kB
prinseq.snakefile
2.2 kB
UPDATING.md
1.7 kB
UPDATING.sh
496 Bytes
UPGRADE.md
2.1 kB
Workshops
INRB2023.md
8.9 kB
README.md
206 Bytes
SAGC2021.md
23.6 kB
fastp_788707_20180129.html
556.1 kB
images
bandage.png
210.8 kB
k119_21323.allsamples.png
59.9 kB
k119_21323.threesamples.png
108.8 kB
megahit_bins.png
16.0 kB
snakemake
README.md
526 Bytes
envs
focus.yaml
55 Bytes
kraken.yaml
57 Bytes
megahit.yaml
57 Bytes
minimap.yaml
74 Bytes
prinseq.yaml
86 Bytes
samtools.yaml
58 Bytes
superfocus.yaml
61 Bytes
envs.zip
1.6 kB
process_metagenomesSAGC.snakefile
11.1 kB
process_metagenomesSAGC_conda.snakefile
11.5 kB
_config.yml
25 Bytes
tRNA_rRNA
README.md
2.1 kB
tRNA_rRNA.pdf
19.0 kB