.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
.TH BIO-RAINBOW "1" "July 2018" "bio-rainbow 2.0.4" "User Commands"
.SH NAME
bio-rainbow \- clustering and assembling short reads for bioinformatics
.SH SYNOPSIS
.B rainbow
\fI\,<cmd> \/\fR[\fI\,options\/\fR]
.SH DESCRIPTION
rainbow 2.0.4 \fB\-\-\fR <ruanjue@gmail.com, chongzechen@gmail.com>
.IP
cluster
.PP
Input  File Format: paired fasta/fastq file(s)
Output File Format: <seqid:int>\et<cluster_id:int>\et<read1:string>\et<read2:string>
.HP
\fB\-1\fR <string> Input fasta/fastq file, supports multiple '\-1'
.HP
\fB\-2\fR <string> Input fasta/fastq file, supports multiple '\-2' [null]
.TP
\fB\-l\fR <int>
Read length, default: 0 variable
.TP
\fB\-m\fR <int>
Maximum mismatches [4]
.TP
\fB\-e\fR <int>
Exactly matching threshold [2000]
.TP
\fB\-L\fR
Low level of polymorphism
.IP
div
.PP
Input File Format: <seqid:int>\et<cluster_id:int>\et<read1:string>\et<read2:string>
Output File Format: <seqid:int>\et<cluster_id:int>\et<read1:string>\et<read2:string>[\et<pre_cluster_id:int>]
.HP
\fB\-i\fR <string> Input file [stdin]
.HP
\fB\-o\fR <string> Output file [stdout]
.TP
\fB\-k\fR <int>
K_allele, min variants to create a new group [2]
.TP
\fB\-K\fR <int>
K_allele, divide regardless of frequency when num of variants exceed this value [50]
.TP
\fB\-f\fR <float>
Frequency, min variant frequency to create a new group [0.2]
.IP
merge
.PP
Input File Format: <seqid:int>\et<cluster_id:int>\et<read1:string>\et<read2:string>[\et<pre_cluster_id:int>]
.HP
\fB\-i\fR <string> Input rbasm output file [stdin]
.TP
\fB\-a\fR
output assembly
.HP
\fB\-o\fR <string> Output file for merged contigs, one line per cluster [stdout]
.TP
\fB\-N\fR <int>
Maximum number of divided clusters to merge [300]
.TP
\fB\-l\fR <int>
Minimum overlap when assemble two reads (valid only when '\-a' is opened) [5]
.TP
\fB\-f\fR <float>
Minimum fraction of similarity when assembly (valid only when '\-a' is opened) [0.90]
.TP
\fB\-r\fR <int>
Minimum number of reads to assemble (valid only when '\-a' is opened) [5]
.TP
\fB\-R\fR <int>
Maximum number of reads to assemble (valid only when '\-a' is opened) [300]
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.