biology/filter-fastq 0.0.0.20210527nb2 NetBSD

Filter reads from a FASTQ file using a list of identifiers.

Each entry in the input FASTQ file (or files) is checked against all entries in the identifier list. Matches are included by default, or excluded if the --invert flag is supplied. Paired-end files are kept consistent (in order).

This is almost certainly not the most efficient way to implement this filtering procedure. I tested a few different strategies and this one seemed the fastest. Current timing with 16 processes is about 10 minutes per 1M paired reads with gzip'd input and output, depending on the length of the identifier list to filter by.

usage: filter_fastq.py [-h] [-i INPUT] [-1 READ1] [-2 READ2] [-p NUM_THREADS] [-o OUTPUT] [-f FILTER_FILE] [-v] [--gzip]