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Rainbow v1.0.1 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 > rbdiv.out rbasm -i rbdiv.out -o rbasm.out rainbow merge -a rbasm.out -v rbdiv.out -p 0.002 > merged.txt ## [-p] is the estimated heterogosity rerun_rbasm.pl merged.txt rbdiv.out rbasm.out # the output file 'final_asm.fa' contains the final contigs ---------------------------------------------------------------------------------- rainbow 1.1 -- <ruanjue@gmail.com, chongzechen@gmail.com> Usage: rainbow <cmd> [options] Input File Format: paired fasta/fastq file(s) Output File Format: <seqid:int>\t<cluster_id:int>\t<read1:string>\t<read2:string>[\t<pre_cluster_id:int>] cluster -1 <string> Input fasta/fastq file, supports multiple '-1' -2 <string> Input fasta/fasta file, supports multiple '-2' [null] -l <int> Read length, default: 0 variable -m <int> Maximum mismatches [2] -e <int> Exactly matching threshold [2000] div -i <string> Input file [stdin] -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 ***this procedure should be run after rbasm*** -a <string> Input rbasm output file [stdin] -v <string> Input rainbow divided file [stdin] -p <float> maximum heterozygosity to collapse, should be specifed according to the estimated polymorphism of the species [0.01] -l <int> Minimum overlap to collapse two contigs [100] -n <int> Maximum number of contigs to execute pairwise alignment [50] ---------------------------------------------------------------------------------- rbasm: a greedy assembler to locally assemble each cluster produced by rainbow Local assemble fragments around restriction sites 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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