=====Software:=====
[[https://sites.google.com/site/renxwise/home/qridge QRidge]]

=====Author:=====
Xianwen Ren, [[http://www.ipbcams.ac.cn Institute of Pathogen Biology, CAMS]]

=====Function:=====
Given a set of RNA-Seq data, QRidge assembles the short reads into long full-length transcripts.

=====Usage:=====
%%QRidge.pl <Fasta> <KmerSize> <MinCoverage> <MinContigLength> <Mode:Comprehensive|Concise>%%
Here,
<Fasta>:                      Specify the path to the reads file, requiring the fasta format; For paired-end sequencing, the two reads files should be concatenated to one single fasta file.
<KmerSize>:                   Specify the size of kmers. The values can be any number smaller than the read length, generally 25.
<MinCoverage>:                Specify the minimum allowed frequency for each kmer. Kmers with frequency smaller than MinCoverage will be deleted. MinCoverage=1 is the most sensitive.
<MinContigLength>:            Only contigs longer than MinContigLength will be printed.
<Mode:Comprehensive|Concise>: The program provides two assembly modes. One is specified by 0, i.e., the comprehensive mode; the other is specified by 1, i.e., the concise mode. Comprehensive mode allows repeated kmers within and between contigs; concise mode only allows repeated kmers within contigs but does not allow repeated kmers between contigs. Comprehensive mode is more sensitive but slower.

An example: 
%%QRidge.pl reads.fasta 25 1 100 0 >contigs.fasta%%

=====Reference:=====
Xianwen Ren and Qi Jin. Restoring transcriptomes from shotgun RNA-Seq data through quantitative sequence transformation. Submitted.