---
name: "bio-rainbow"
section: "1"
platform: "linux"
package: "bio-rainbow"
version: "2.0.4+dfsg-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/bio-rainbow"
---

# bio-rainbow(1)

clustering and assembling short reads for bioinformatics

## 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' \[null\]

- **-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) \[300\]

## AUTHOR

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