.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.12.
.TH YANAGIBA "1" "June 2020" "yanagiba 1.0.0" "User Commands"
.SH NAME
yanagiba \- Filters low quality Oxford Nanopore reads basecalled with Albacore
.SH DESCRIPTION
usage: yanagiba [\-h] \fB\-i\fR INFILE [\-s SUMMARYFILE] [\-o OUTFILE] [\-l MINLEN]
.IP
[\-q MINQUAL] [\-\-headtrim HEADTRIM] [\-\-tailtrim TAILTRIM] [\-u]
.PP
Filter and slice Nanopore reads which have been basecalled with Albacore.
Takes fastq.gz and an Albacore summary file.
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-i\fR INFILE, \fB\-\-infile\fR INFILE
Input fastq.gz file.
.TP
\fB\-s\fR SUMMARYFILE, \fB\-\-summaryfile\fR SUMMARYFILE
Albacore summary file with header row.
.TP
\fB\-o\fR OUTFILE, \fB\-\-outfile\fR OUTFILE
Write filtered reads to this file in .bgz format.
.TP
\fB\-l\fR MINLEN, \fB\-\-minlen\fR MINLEN
Exclude reads shorter than this length. Default: 0
.TP
\fB\-q\fR MINQUAL, \fB\-\-minqual\fR MINQUAL
Minimum quality score to retain a read. Default: 10
.TP
\fB\-\-headtrim\fR HEADTRIM
Trim x bases from beginning of each read. Default: 0
.TP
\fB\-\-tailtrim\fR TAILTRIM
Trim x bases from end of each read. Default: None
.TP
\fB\-u\fR, \fB\-\-forceunique\fR
Enforce unique reads. Only store first instance of a
read from fastq input where readID occurs multiple
times.
.SH AUTHOR
 This manpage was written by Nilesh Patra for the Debian distribution and
 can be used for any other usage of the program.