Provided a single, or list of, regular expressions, filter out all reads from a given fastq file which match said expression(s).
One use case could be dropping reads with a large amount of poly-A sequences:
python fqfilter.py -f Sample01.fastq -d "[A]{25}"
Or perhaps you have a specific adapter at the start of the read that you'd like to isolate
python fqfilter.py -f Sample01.fastq -k "^ATCGGCTA"
And you can also do both at once!
python fqfilter.py -f Sample01.fastq -k "^ATCGGCTA" -d "[A]{25}"
-f/--fastq |
Input fastq file to filter |
-p/--pair |
Input pair of fastqs. R1 then R2. Files will be syncronized in the ouput for safety of downstream processing! |
-k/--keep |
Regex expression(s) to keep |
-d/--drop |
Regex expression(s) to drop |
-s/--sync |
|
-v/--verbose |
Debug output |
Built on Python 3.11, but may be fine back as far as 3.7
Needs the BioPython package