16 lines
760 B
Text
16 lines
760 B
Text
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Filter reads from a FASTQ file using a list of identifiers.
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Each entry in the input FASTQ file (or files) is checked against all
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entries in the identifier list. Matches are included by default, or
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excluded if the --invert flag is supplied. Paired-end files are kept
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consistent (in order).
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This is almost certainly not the most efficient way to implement this
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filtering procedure. I tested a few different strategies and this one
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seemed the fastest. Current timing with 16 processes is about 10
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minutes per 1M paired reads with gzip'd input and output, depending on
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the length of the identifier list to filter by.
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usage: filter_fastq.py [-h] [-i INPUT] [-1 READ1] [-2 READ2] [-p NUM_THREADS]
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[-o OUTPUT] [-f FILTER_FILE] [-v] [--gzip]
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