yanagiba1
Filters low quality oxford nanopore reads basecalled with albacore
Overview
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.
Releases
Unchanged in 3 releases since Debian 11 (Bullseye).