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BIO-RAINBOW(1) User Commands BIO-RAINBOW(1)

NAME

bio-rainbow - clustering and assembling short reads for bioinformatics

SYNOPSIS

rainbow <cmd> [options]

DESCRIPTION

rainbow 2.0.4 -- <ruanjue@gmail.com, chongzechen@gmail.com>

cluster

Input File Format: paired fasta/fastq file(s) Output File Format: <seqid:int>\t<cluster_id:int>\t<read1:string>\t<read2:string>

-1 <string> Input fasta/fastq file, supports multiple '-1'

-2 <string> Input fasta/fastq file, supports multiple '-2' [null]

Read length, default: 0 variable
Maximum mismatches [4]
Exactly matching threshold [2000]
Low level of polymorphism
div

Input File Format: <seqid:int>\t<cluster_id:int>\t<read1:string>\t<read2:string> Output File Format: <seqid:int>\t<cluster_id:int>\t<read1:string>\t<read2:string>[\t<pre_cluster_id:int>]

-i <string> Input file [stdin]

-o <string> Output file [stdout]

K_allele, min variants to create a new group [2]
K_allele, divide regardless of frequency when num of variants exceed this value [50]
Frequency, min variant frequency to create a new group [0.2]
merge

Input File Format: <seqid:int>\t<cluster_id:int>\t<read1:string>\t<read2:string>[\t<pre_cluster_id:int>]

-i <string> Input rbasm output file [stdin]

output assembly

-o <string> Output file for merged contigs, one line per cluster [stdout]

Maximum number of divided clusters to merge [300]
Minimum overlap when assemble two reads (valid only when '-a' is opened) [5]
Minimum fraction of similarity when assembly (valid only when '-a' is opened) [0.90]
Minimum number of reads to assemble (valid only when '-a' is opened) [5]
Maximum number of reads to assemble (valid only when '-a' is opened) [300]

AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

July 2018 bio-rainbow 2.0.4