NOTE: this repo is outdated. Please use the fully reimplemented and faster version called decontanimate
Decontaminate FastQ files by mapping with BWA-MEM against a given source.
Performs a mapping of given SR/PE reads (gzip supported) with BWA-MEM against given source of contamination and produces an (unsorted) BAM file with contaminated reads (one mate mapping suffices to make pair count as contamination) and new, gzipped fastq file(s) with uncontaminated reads.
Needs samtools and BWA(-MEM) installed.
If minimum coverage is not met, the read is treated as unaligned.
- SE aligned
- SE unaligned
- SE secondary
- SE aligned below mincov
- PE both aligned
- PE both unaligned
- PE one aligned
- PE both aligned secondary
- Run
samtools fixmate(paranoia) followed by samtools fastq -F, removing any unmapped read or read with unmapped pair (option) and secondary alignments