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http://maq.sourceforge.net/

A set of programs that map and assemble fixed-length Solexa/SOLiD reads in a fast and accurate way.

Proper citation: Maq (RRID:SCR_005485) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/fas-dpd/

Software program to design degenerate primers for PCR.

Proper citation: FAS-DPD (RRID:SCR_003068) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/gemsim/

A software package for generating realistic simulated next-generation genome sequencing reads with quality score values. The software is written in Python with a command-line user interface.

Proper citation: GemSIM (RRID:SCR_000167) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/hlaseq/

An open-source software tool for accurate genotyping the human HLA genes from Illumina GA high-throughput sequencing data.

Proper citation: HLASeq (RRID:SCR_004185) Copy   

•   Source: SciCrunch Registry

http://svdetect.sourceforge.net/Site/Home.html

Software application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies. This tool aims to identify structural variations with both clustering and sliding-window strategies, and helping in their visualization at the genome scale. It is compatible with SOLiD and Illumina (>=1.3) reads.

Proper citation: SVDetect (RRID:SCR_010812) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/saskprimerfs/

Software pipeline for designing gene family specific PCR primers. It infers intronic regions of a target species and design for them by utilizing DNA sequence information from a reference organism.

Proper citation: SaskPrimerFS (RRID:SCR_003159) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/primerdesigner/

High throughput PCR primer design software. Target regions defined through a rich set of descriptors, such as Ensembl accessions and arbitrary genomic coordinates, may be specified. Primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the specified target regions. As part of the tiling process, primer pairs are computationally screened to meet the criteria for success with one of two PCR amplification protocols.

Proper citation: JCVI Primer Designer (RRID:SCR_003275) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/popbam/

A tool to perform evolutionary or population-based analyses of next-generation sequencing data. POPBAM takes a BAM file as its input and can compute many widely used evolutionary genetics measures in sliding windows across a genome.

Proper citation: POPBAM (RRID:SCR_000464) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/srma/

A post-alignment micro re-aligner for next-generation high throughput sequencing data.

Proper citation: SRMA (RRID:SCR_000669) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/qips/

A software package for analyzing ChIP-seq (Chromatin ImmunoPrecipitation on sequencing) data that finds enriched regions of arbitrary lengths and is therefore especially suited for analyzing ChIP-seq of histone marks or polymerase.

Proper citation: qips (RRID:SCR_001092) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/dprimer/

A command line software utility for designing degenerate PCR primers against multiple, aligned sequences. Its primary use case is searching for a family of related pathogens in a host tissue sample.

Proper citation: dprimer (RRID:SCR_000050) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/hiahia/

A sequence alignment tool to align both short and long reads to a reference genome. HIA has two indexes, a hash table index and a suffix array index. The hash table is capable of the direct lookup of a q-gram and the suffix array is very fast in the lookup of a variable length q-gram. Our experiments show that the hybrid of hash table and suffix array is useful at the perspective of speed to map NGS sequencing reads to a reference genome sequence.

Proper citation: HIA (RRID:SCR_006865) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/simhtsd/

Software that given a reference sequence, will create a large set of short nucleotide reads, simulating the output from today''s high-throughput DNA sequencers, such as the Illumina Genome Analyzer II.

Proper citation: simhtsd (RRID:SCR_006822) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/b-o-s-s/

Batch primer selection software program designed to select PCR oligos for gap closure for assemblies containing a large number of gaps. It will select oligos for gap closure of both contig and scaffold gaps.

Proper citation: Batch Oligo Selection Script (RRID:SCR_002808) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/htqc/

A software toolkit including statistics tool for illumina high-throughput sequencing data, and filtration tools for sequence quality, length, tail quality, etc..

Proper citation: HTQC (RRID:SCR_006448) Copy   

•   Source: SciCrunch Registry