Binning

Bin the contigs in bins to obtain partial reconstructed genomes

Source the configuration file:

source conf_cluster.conf

Upload bowtie2 module:

module load profile/bioinf
module load autoload bowtie2/2.2.9

Write the abundance list file:

for i in $SAMPLE_LIST; do cat $FILT_READS/filtered.$i.R1.fastq $FILT_READS/filtered.$i.R2.fastq $FILT_READS/filtered.single.$i.fastq > $FILT_READS/cat.filtered.$i.fastq; echo $FILT_READS/cat.filtered.$i.fastq >> list_file_maxbin.txt; done

Create output folder for binning output:

mkdir -p $BINN
mv list_file_maxbin.txt  $BINN
cd $BINN

Run MaxBin on the co-assembly:

run_MaxBin.pl -contig $ASSEMB_READS/d.$PRJ_NAME.idba/contig.fa -reads_list list_file_maxbin.txt -out bin.$PRJ_NAME