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rainbow - manual page for rainbow 2.0.4 -- <ruanjue@gmail.com,

RAINBOW(1) User Commands RAINBOW(1)

NAME

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

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]
-l <int>
Read length, default: 0 variable
-m <int>
Maximum mismatches [4]
-e <int>
Exactly matching threshold [2000]
-L
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 <int>
K_allele, min variants to create a new group [2]
-K <int>
K_allele, divide regardless of frequency when num of variants exceed this value [50]
-f <float>
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]
-a
output assembly
-o <string> Output file for merged contigs, one line per cluster [stdout]
-N <int>
Maximum number of divided clusters to merge [300]
-l <int>
Minimum overlap when assemble two reads (valid only when '-a' is opened) [5]
-f <float>
Minimum fraction of similarity when assembly (valid only when '-a' is opened) [0.90]
-r <int>
Minimum number of reads to assemble (valid only when '-a' is opened) [5]
-R <int>
Maximum number of reads to assemble (valid only when '-a' is opened) [300]
Usage: rainbow <cmd> [options]
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]
-l <int>
Read length, default: 0 variable
-m <int>
Maximum mismatches [4]
-e <int>
Exactly matching threshold [2000]
-L
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 <int>
K_allele, min variants to create a new group [2]
-K <int>
K_allele, divide regardless of frequency when num of variants exceed this value [50]
-f <float>
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]
-a
output assembly
-o <string> Output file for merged contigs, one line per cluster [stdout]
-N <int>
Maximum number of divided clusters to merge [300]
-l <int>
Minimum overlap when assemble two reads (valid only when '-a' is opened) [5]
-f <float>
Minimum fraction of similarity when assembly (valid only when '-a' is opened) [0.90]
-r <int>
Minimum number of reads to assemble (valid only when '-a' is opened) [5]
-R <int>
Maximum number of reads to assemble (valid only when '-a' is opened) [300]

SEE ALSO

The full documentation for rainbow is maintained as a Texinfo manual. If the info and rainbow programs are properly installed at your site, the command
info rainbow
should give you access to the complete manual.
August 2015 rainbow 2.0.4 -- <ruanjue@gmail.com, chongzechen@gmail.com>