bio-rainbow1

Usage

Overview

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]