Program to detect and correct errors in DNA sequencing reads. Using a maximum likelihood approach incorporating quality values and nucleotide specific miscall rates,
PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone an...
deFuse is a software package for gene fusion discovery using RNA-Seq data. The software uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries. The software also employs a number of heuristic filters in an attempt to red...
PASS performs fast gapped and ungapped alignments of short DNA sequences onto a reference DNA, typically a genomic sequence. It is designed to handle a huge amount of reads such as those generated by Solexa, SOLiD or 454 technologies. The algorithm is based on a data structure that hold...
De novo transcriptome assembler for very short reads
De novo transcriptome assembler for very short reads
De novo transcriptome assembler for very short reads
Novoalign is a program for mapping short reads from the Illumina/SOLiD sequencing platform(s) to a reference genome.
Package for aligning short reads to reference genomes
PerM (Periodic Seed Mapping) uses periodic spaced seeds to significantly improve mapping efficiency for large reference genomes when compared to state-of-the-art programs.