Procedure for removing contaminants from paired-end sequence data. The bwa-mem algorithm is used to map reads against a database of contaminants, a small Perl one-liner is used to filter out reads that map to the contaminants, the SAM data is converted to BAM format, which is then fed (via process substitution) to Tophat's bam2fastx to convert b…

fq-strip-contam.sh

# -q: output in Fastq format
# -Q: ignore BAM quality flags
# -P: paired-end data
bam2fastx -qQP -o clean.fq <(bwa mem contaminants.fasta reads.1.fq reads.2.fq | \
                             perl -ne '@v = split(/\t/); print if(m/^@/ or ($v[1] & 4 and $v[1] & 8))' | \
                             samtools view -bhS -)