YANAGIBA

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.