table of contents
| YANAGIBA(1) | User Commands | YANAGIBA(1) |
NAME¶
yanagiba - Filters low quality Oxford Nanopore reads basecalled with Albacore
DESCRIPTION¶
usage: yanagiba [-h] -i INFILE [-s SUMMARYFILE] [-o OUTFILE] [-l MINLEN]
- [-q MINQUAL] [--headtrim HEADTRIM] [--tailtrim TAILTRIM] [-u]
Filter and slice Nanopore reads which have been basecalled with Albacore. Takes fastq.gz and an Albacore summary file.
optional arguments:¶
- -h, --help
- show this help message and exit
- -i INFILE, --infile INFILE
- Input fastq.gz file.
- -s SUMMARYFILE, --summaryfile SUMMARYFILE
- Albacore summary file with header row.
- -o OUTFILE, --outfile OUTFILE
- Write filtered reads to this file in .bgz format.
- -l MINLEN, --minlen MINLEN
- Exclude reads shorter than this length. Default: 0
- -q MINQUAL, --minqual MINQUAL
- Minimum quality score to retain a read. Default: 10
- --headtrim HEADTRIM
- Trim x bases from beginning of each read. Default: 0
- --tailtrim TAILTRIM
- Trim x bases from end of each read. Default: None
- -u, --forceunique
- Enforce unique reads. Only store first instance of a read from fastq input where readID occurs multiple times.
AUTHOR¶
This manpage was written by Nilesh Patra for the Debian
distribution and
can be used for any other usage of the program.
| June 2020 | yanagiba 1.0.0 |