NAME
to_fasta.py - Remove adapters and collapse reads from FASTQ to FASTA
DESCRIPTION
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)
- -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'
AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and
can be used for any other usage of the program.