Extension of the short read analysis pipeline SHORE. SHOREmap supports genome-wide genotyping and candidate-gene sequencing in a single step through analysis of deep sequencing data from a large pool of recombinants.
Stand-alone scaffolder of pre-assembled contigs using paired-read data.
SSPACE standard is a stand-alone program for scaffolding pre-assembled contigs using NGS paired-read data.
Uses a hybrid mapping algorithm and a detailed statistical model to achieve both speed and sensitivity, particularly when reads include sequence variation.
stampy is a package for mapping short Illumina reads onto a reference genome. It can bs used for genomic resequencing, RNA-Seq a...
An alternative to Cufflinks, MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates the expression level of alternatively spliced genes.
We introduce a second generation splice detection algorithm, MapSplice, whose focus is high sensitivity and specificity in the detection of splices as well as CPU and memory efficiency. MapSplice can be applied to both short (<75 bp) and long reads (75 bp). MapSplice is not dependent...
An unsupervised learning method, which finds, in an unbiased fashion, commonly occurring chromatin signatures in both tiling microarray and sequencing data.
RazerS allows the user to align sequencing reads of arbitrary length using either the Hamming distance or the edit distance. The tool can work either lossless or with a user-defined loss rate at higher speeds.
mrsFAST is a micro-read substitution-only Fast Alignment Search Tool. mrsFAST is a cache-oblivous short read mapper that optimizes cache usage to get higher performance.