Bowtie2 - Filter Reads From ReferenceΒΆ
Remove reads that do not map to the reference, and so may be caused by contamination in lab processing. Alternatively, using keep: False configuration removes all fragments that belongs to reference, and so is suitable to remove contamination caused by host with known genome, e.g. human fragments.
Location
- Filepath: <SnakeLines_dir>/rules/paired_end/reads/preprocess/decontaminated/bowtie2.snake
- Rule name: bowtie2__filter_reads_from_reference
Input(s):
- r1: Left side of sequenced fragments in gzipped fastq format
- r2: Right side of sequenced fragments in gzipped fastq format
- index_files: List of reference bowtie2 databases
Output(s):
- r1: Left side of filtered fragments in gzipped fastq format
- r2: Right side of filtered fragments in gzipped fastq format