Genome binning of the gold standard pooled assembly Software: CONCOCTSoftwareVersion: 1.0.0DataURL: https://data.cami-challenge.org/participateSoftwareURL: https://github.com/BinPro/CONCOCTDockerImage: quay.io/biocontainers/concoct:1.0.0--py37h88e4a8a_5IsBiobox: NoShortReadsUsed: TrueLongReadsUsed: FalseCommandUsed: 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 ; donefor i in {0..63}; do samtools view -b sample_${i}.sam -o anonymous_reads_sample_${i}.bam & donefor i in {0..63}; do samtools sort anonymous_reads_sample_${i}.bam -o anonymous_reads_sample_${i}.sorted.bam ; donefor i in {0..63}; do samtools index anonymous_reads_sample_${i}.sorted.bam ; donecut_up_fasta.py anonymous_gsa_pooled.fasta -c 10000 -o 0 --merge_last -b contigs_10K.bed > contigs_10K.faconcoct_coverage_table.py contigs_10K.bed /host/benchmarking/fmeyer/output/bowtie2/mouse_gut/sorted_bam/anonymous_reads_sample_*.sorted.bam > coverage_table.tsvconcoct --composition_file contigs_10K.fa --coverage_file coverage_table.tsv -bmerge_cutup_clustering.py clustering_gt1000.csv > clustering_merged.csv