Software:

QRidge

Author:

Xianwen Ren, 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.
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