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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/fitgcp/

Software providing a framework for fitting mixtures of probability distributions to genome coverage profiles.

Proper citation: fitGCP (RRID:SCR_006741) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/gasic/

A method to correct read alignment results for the ambiguities imposed by similarities of genomes.

Proper citation: GASiC (RRID:SCR_006765) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/atlas-link/

Software that implements a greedy algorithm and uses graph theory to link and orient assembled existing contigs quickly and accurately using mate pair information.

Proper citation: Next-gen Sequencing Scaffolding Tool (RRID:SCR_006762) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/quasr/

A lightweight software pipeline written to process and analyse next-generation sequencing (NGS) data from Illumina, 454, and Ion Torrent platforms. Although originally written for viral data, it is generic enough to work on any NGS dataset. Functions include: duplicate removal, demultiplexing, primer-removal, quality-assurance (QA) graphing, quality control (QC), consensus-generation, minority-variant determination, minority-variant graphing.

Proper citation: QUASR (RRID:SCR_006820) 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://bionerds.sourceforge.net/

A named entity recognizer for the recovery of bioinformatics databases and software from primary literature. The entity recognizer achieved an F-measure of between 63% and 91% on different datasets (63%78% at the document level). Results from full-text literature analysis for both Genome Biology and BMC Bioinformatics journals are available as well as a full list of references and links for the various major resources mentioned. Data generated data can be used for exploration of bioinformatics database and software usage. This tool makes heavy use of GATE (version 6.1). It can be run in sandbox mode, which means a installation of GATE is not a prerequisite, but you will instead need to point the config to a unzipped gate_plugins directory instead (located in the bin/BMC_Files directory).

Proper citation: bioNerDS (RRID:SCR_006784) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/virmid/

A Java based variant caller designed for disease-control matched samples. Virmid is also specialized for identifying potential within individual contamination where the disease sample cannot be purified enough. While the SNP calling rate is severely compromised with this heterogeneity, Virmid can uncover SNPs with low allele frequency by considering the level of contamination (alpha). The important features of Virmid are: * Estimation of accurate proporation of control sample in a (mixed) disease sample * Improved SNP and somatic mutation calling with regard to the estimated proportion

Proper citation: Virmid (RRID:SCR_006780) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/bigpre/

A quality assessment software package for next-genomics sequencing data.

Proper citation: BIGpre (RRID:SCR_006781) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/taxoassignement/

Software tool for the taxonomic assignment of Next Generation Sequencing reads using multiple reference taxonomy.

Proper citation: TaxoAssignement (RRID:SCR_006814) Copy   

•   Source: SciCrunch Registry

http://deconseq.sourceforge.net/

Software tool to automatically detect and efficiently remove sequence contaminations from genomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface. The user can upload FASTA or FASTQ files and select the databases used for contamination screening, including seven human genomes, bacterial genomes, and viral genomes. The user can set the thresholds interactivly and see the results directly using the functionality of the graphical interface. The results can be downloaded in joined or separated files in different formats. The coverage-identity plots provide additional information that can guide the selections of the thresholds using color coded points and connecting lines.

Proper citation: DeconSeq (RRID:SCR_007006) Copy   

•   Source: SciCrunch Registry

http://mcx.sourceforge.net/

A Monte Carlo simulation software for photon migration in 3D turbid media. It uses Graphics Processing Units (GPU) based massively parallel computing techniques and is extremely fast compared to the traditional single-threaded CPU-based simulations. Using an nVidia 8800GT graphics card (14MP/114Cores), the acceleration is about 300x~400x compared to a single core of Xeon 5120 CPU; this ratio can be as high as 700x with a GTX 280 GPU and 1400x with a GTX 470.

Proper citation: Monte Carlo eXtreme (RRID:SCR_007001) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/particlecall/

A base-calling algorithm for Illumina DNA sequencing.

Proper citation: ParticleCall (RRID:SCR_001103) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/sparseassembler/

Software for memory-efficient genome assembly. It utilizes sparse k-mer.

Proper citation: SparseAssembler (RRID:SCR_001100) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/cuda-ec/

A fast parallel error correction tool for short reads.

Proper citation: CUDA-EC (RRID:SCR_001090) 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://crossmap.sourceforge.net/

A software program for convenient conversion of genome coordinates (or annotation files) between different assemblies. It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF. It is designed to liftover genome coordinates between assemblies. It?s not a program for aligning sequences to reference genome. CrossMap is not recommend for converting genome coordinates between species.

Proper citation: CrossMap (RRID:SCR_001173) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/apps/mediawiki/breakway/index.php

A suite of software programs that take aligned genomic data and report structural variation breakpoints. Features include: * Takes in BAM formatted input, the current standard for genomic alignments. * Compatible with standard output from major alignment algorithms such as BFAST, BWA, MAQ, et cetera. * Capable of analyzing data from any major platform--Solexa, SOLiD, 454, et cetera. * Empirically identifies structural variation breakpoints. * Highly specific analysis generates very few false positives. * Includes a suite of downstream tools for annotating identified breakpoints and reducing false positives.

Proper citation: Breakway (RRID:SCR_001180) Copy   

•   Source: SciCrunch Registry

https://gitlab.sib.swiss/EPD/chipseq

Set of software modules for performing common ChIP-seq data analysis tasks across the whole genome, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. The tools are designed to be simple, fast and highly modular. Each program carries out a well-defined data processing procedure that can potentially fit into a pipeline framework. ChIP-Seq is also freely available on a Web interface.

Proper citation: ChIP-seq (RRID:SCR_001237) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ngsrich/

Software for target enrichment performance for next-generation sequencing.

Proper citation: NGSrich (RRID:SCR_001333) Copy   

•   Source: SciCrunch Registry