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Rainbow v2.0.4
Description
===========
Rainbow package consists of several programs used for RAD-seq related
clustering and de novo assembly.
Installation
============
Type 'make' to compile Rainbow package. You can copy the executables/scripts
to your specific location (e.g. a directory in your $PATH). Or you can set
the PATH environment that leads to this directory.
Usage of Rainbow package
========================
EXAMPLE: a typical use of Rainbow step by step
rainbow cluster -1 1.fq -2 2.fq > rbcluster.out 2> log
rainbow div -i rbcluster.out -o rbdiv.out
rainbow merge -o rbasm.out -a -i rbdiv.out -N500
The final output file of 'rainbow merge -a' is based on the final merged
clusters. Each cluster has been locally assembled by 'rainbow merge -a'. For
each cluster, rainbow outputs all assembled contigs seperated by '//' for each
record:
E clusterID
C contigID1
L length
S sequence
N #reads
R readIDs
//
C contigID2
L length
S sequence
N #reads
R readIDs
.
.
.
We have also provided four simple perl scripts that can be used to extract the assembly
information: select_all_rbcontig.pl, select_best_rbcontig.pl, select_sec_rbcontig.pl, select_best_rbcontig_plus_read1.pl
select_all_rbcontig.pl extracts all the assembled contigs, i.g., all the
records
select_best_rbcontig.pl and select_sec_rbcontig.pl extract the longest and
the longest plus the second longest contigs for the final clusters,
respectively
select_best_rbcontig_plus_read1.pl, as select_best_rbcontig.pl, it extracts the longest contig for each cluster. Besides, it also outputs the read1. If read1 overlaps with the contig, it joins the two as a whole. If read1 does not overlap with the contig, it pads 10 'X' to join the read1 and the contig, thus generating a long contig.
----------------------------------------------------------------------------------
rainbow 2.0.3 -- <ruanjue@gmail.com, chongzechen@gmail.com>
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 rainbow cluster output 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 rainbow div output file [stdin]
-a output assembly
-o <string> Output file [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]
----------------------------------------------------------------------------------
rbasm: a greedy assembler to locally assemble each cluster produced by rainbow or the other
tools. This has been integrated into the merge module. Please always open '-a' option when running
'rainbow merge'.
Local assemble fragments around restriction sites
NOTE: the input file format should be: <seqid:int>\t<cluster_id:int>\t<read1:string>\t<read2:string>[\t<pre_cluster_id:int>]
Usage: rbasm [options]
-i <string> Input file [STDIN]
-o <string> Output file [STDOUT]
-l <int> Minium length of overlap [5]
-s <float> Minium similiarity of overlap [0.90]
-r <int> Minium reads to execute assembly [5]
-R <int> Maxium reads to execute assembly [200]
----------------------------------------------------------------------------------
<Obsoleted> rbmergetag: a program merges divided results to evaluate clustering performance.
Users should omit this program when de novo assembling RAD-seq reads.
Usage: rbmergetag [options]
Options:
-i <string> Input file name [stdin]
-o <string> Output file name [stdout]
-j <cns|merge> Job type, cns: consensus, merge: merging, [merge]
-m <int> Maximum mismatches to merge two groups [1]
-h Show this document
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Change log:
===========
v2.0.1: README and usage infomation updated
v2.0.2: 'merge' options are riched. The 'merge' assembly work can be customized like rbasm now. Thanks Ross Whetten in NCSU for advicing this.
v2.0.3: changed the name of script 'select_best_rbcontig2.pl' to 'select_best_rbcontig_plus_read1.pl', and documented it.
v2.0.4: fixed a bug that rainbow cannot be compiled in Mac OS
