.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH PIZZLY "1" "November 2020" "pizzly version: 0.37.3" "User Commands"
.SH NAME
pizzly \- pizzly
.SH DESCRIPTION
pizzly
======
.PP
SYNOPSIS
.PP
DESCRIPTION
.PP
REQUIRED ARGUMENTS
.IP
FUSION STRING
.PP
OPTIONS
.HP
\fB\-h\fR, \fB\-\-help\fR
.IP
Display the help message.
.HP
\fB\-\-version\-check\fR BOOL
.IP
Turn this option off to disable version update notifications of the
application. One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO.
Default: 1.
.HP
\fB\-k\fR INTEGER
.IP
k\-mer size used in kallisto
.HP
\fB\-a\fR, \fB\-\-align\-score\fR INTEGER
.IP
Maximum number of mismatches allowed (default: 2)
.HP
\fB\-i\fR, \fB\-\-insert\-size\fR INTEGER
.IP
Maximum fragment size of library (default: 400)
.HP
\fB\-o\fR, \fB\-\-output\fR STRING
.IP
Prefix for output files
.HP
\fB\-G\fR, \fB\-\-gtf\fR STRING
.IP
Annotation in GTF format
.HP
\fB\-C\fR, \fB\-\-cache\fR STRING
.IP
File for caching annotation (created if not present, otherwise
reused from previous runs)
.HP
\fB\-F\fR, \fB\-\-fasta\fR STRING
.IP
Fasta reference
.HP
\fB\-\-ignore\-protein\fR
.IP
Ignore any protein coding information in annotation
.HP
\fB\-\-version\fR
.IP
Display version information.
.PP
VERSION
.IP
Last update:
pizzly version: 0.37.3
SeqAn version: 2.4.0
.PP
SeqAn version: 2.4.0