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.
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.
Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that expl...
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...
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.
A workflow combining a series of time- and memory-efficient motif analysis tools to extract motifs from full-size collections of peaks as generated by ChIP-seq, ChIP-chip or other ChIP-X technologies.