bowtie2-loop-script

#!/bin/bash

# A simple loop to serially map all samples against the bowtie2 indices.

# how many threads should each mapping task use?
NUM_THREADS=24

for sample in `ls /home/marcolabuser/Zach/LSU_Metagenomics/*_forward_paired_control.fq.gz`
do
    dir="/home/marcolabuser/Zach/LSU_Metagenomics"
    base=$(basename $sample "_forward_paired_control.fq.gz")
    
    #use echo command to make sure the right files are being used 
    echo "bowtie2 \
    --threads $NUM_THREADS \
    -x /home/marcolabuser/Zach/LSU_Metagenomics/bowtie_index/contigs/contigs \
    -1 ${dir}/${base}_forward_paired_control.fq.gz -2 ${dir}/${base}_reverse_paired_control.fq.gz \
    --no-unal \
    -S ${dir}/bowtie_index/${base}.sam \
    --sensitive \
    2>${dir}/bowtie_index/${base}_alignment.log"
    
    #perform bowtie2 alignment in sensitive mode, write STDERR to logfile 
    bowtie2 \
    --threads $NUM_THREADS \
    -x /home/marcolabuser/Zach/LSU_Metagenomics/bowtie_index/contigs/contigs \
    -1 ${dir}/${base}_forward_paired_control.fq.gz \
    -2 ${dir}/${base}_reverse_paired_control.fq.gz \
    --no-unal \
    -S ${dir}/bowtie_index/${base}.sam \
    --sensitive \
    2>${dir}/bowtie_index/${base}_alignment.log
    
    #generate and format BAM file from SAM file  
    samtools view -F 4 -bS ${dir}/bowtie_index/${base}.sam > ${dir}/bowtie_index/${base}-RAW.bam
    
    anvi-init-bam ${dir}/bowtie_index/${base}-RAW.bam -o ${dir}/bowtie_index/${base}.bam
    
    #delete unnecessary files 
    rm ${dir}/bowtie_index/${base}.sam ${dir}/bowtie_index/${base}-RAW.bam

done