table of contents
| TO_FASTA.PY(1) | User Commands | TO_FASTA.PY(1) |
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.
| March 2020 | to_fasta.py 1.1 |