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This is the command bio-rainbow that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


rainbow - manual page for rainbow 2.0.4 -- <[email protected], [email protected]>

SYNOPSIS


rainbow <cmd> [options]

DESCRIPTION


rainbow 2.0.4 -- <[email protected], [email protected]>

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]

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