CONCOCT 1.0.0 genome binning of the CAMI 2 Mouse Gut Toy data set, samples 0-63, gold standard pooled assembly

Genome binning of the gold standard pooled assembly
Software: CONCOCT
SoftwareVersion: 1.0.0
DataURL: https://data.cami-challenge.org/participate
SoftwareURL: https://github.com/BinPro/CONCOCT
DockerImage: quay.io/biocontainers/concoct:1.0.0--py37h88e4a8a_5
IsBiobox: No
ShortReadsUsed: True
LongReadsUsed: False
CommandUsed: 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
for i in {0..63}; do samtools view -b sample_${i}.sam -o anonymous_reads_sample_${i}.bam & done
for i in {0..63}; do samtools sort anonymous_reads_sample_${i}.bam -o anonymous_reads_sample_${i}.sorted.bam ; done
for i in {0..63}; do samtools index anonymous_reads_sample_${i}.sorted.bam ; done
cut_up_fasta.py anonymous_gsa_pooled.fasta -c 10000 -o 0 --merge_last -b contigs_10K.bed > contigs_10K.fa
concoct_coverage_table.py contigs_10K.bed /host/benchmarking/fmeyer/output/bowtie2/mouse_gut/sorted_bam/anonymous_reads_sample_*.sorted.bam > coverage_table.tsv
concoct --composition_file contigs_10K.fa --coverage_file coverage_table.tsv -b
merge_cutup_clustering.py clustering_gt1000.csv > clustering_merged.csv