to_fasta.py1
Remove adapters and collapse reads from fastq to fasta
Overview
usage: to_fasta.py [-h] [-3 SEQ] [-5 SEQ] [--trim-5p BP] [--trim-3p BP]
-
[--seed-5p BP] [--seed-3p BP] [-m BP] [-x BP] [-s] [-B] [-a] FASTQ
Remove adapters and collapse reads from FASTQ to FASTA
positional arguments:
- FASTQ
-
including stdin or compressed file {zip,gz,tar,bz}
optional arguments:
-
-h, --help -
show this help message and exit
-
-3 SEQ -
3'adapter sequence
-
-5 SEQ -
5'adapter sequence
-
--trim-5p BP -
trim specified number of bases from 5'ends
-
--trim-3p BP -
trim specified number of bases from 3'ends
-
--seed-5p BP -
5' adapter match length in bp (default: 7)
-
--seed-3p BP -
3' adapter match length in bp (default: 7)
-
-m BP -
minimum read length in bp (default: 16)
-
-x BP -
maximum read length in bp (default: 36)
-
-s -
sensitive adapter search with 1 mismatch (default: off)
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-B -
only print the reads with both 5' and 3' adapter matches
-
-a -
print all reads with and without adapter matches if the reads are in the range specified with '-m' and '-x'
Releases
Unchanged in 3 releases since Debian 11 (Bullseye).