table of contents
| 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> |