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http://sourceforge.net/projects/insertionmapper/

A pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data. It consists of four independently working modules: Data Preprocessing, Database Modeling, Dimension Deconvolution and Element Mapping. This pipeline tool is applicable to scenarios requiring analysis of the tremendous output of short reads produced in NGS sequencing experiments of targeted genome sequences.

Proper citation: InsertionMapper (RRID:SCR_004163) Copy   

•   Source: SciCrunch Registry

https://bcbio-nextgen.readthedocs.org/en/latest/

A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis.

Proper citation: bcbio-nextgen (RRID:SCR_004316) Copy   

•   Source: SciCrunch Registry

http://genome.gsc.riken.jp/osc/english/dataresource/

A program to eliminate artifactual reads from next-generation sequencing data sets.

Proper citation: TagDust (RRID:SCR_004175) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/resources/software/artemis/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Free genome browser and annotation tool that allows visualization of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation. Artemis is free software and is distributed under the terms of the GNU General Public License. Artemis is written in Java, and is available for UNIX, Macintosh and Windows systems. It can read EMBL and GENBANK database entries or sequence in FASTA, indexed FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format.

Proper citation: Artemis: Genome Browser and Annotation Tool (RRID:SCR_004267) Copy   

•   Source: SciCrunch Registry

http://snoopcgh.sourceforge.net/

A java desktop application for visualising and exploring comparative genomic hybridization (CGH) data.

Proper citation: SnoopCGH (RRID:SCR_004420) Copy   

•   Source: SciCrunch Registry

http://www.irisa.fr/symbiose/projects/gassst/

Software that finds global alignments of short DNA sequences against large DNA banks. It is able to perform fast gapped alignments and works well for both short and longer reads. It has been tested for reads up to 500bp.

Proper citation: GASSST (RRID:SCR_004413) Copy   

•   Source: SciCrunch Registry

https://github.com/HIITMetagenomics/dsm-framework

Software package providing distributed string mining for High-Throughput Sequencing data that provides a content-based exploration and retrieval method for whole metagenome sequencing samples.

Proper citation: Distributed String Mining Framework (RRID:SCR_004736) Copy   

•   Source: SciCrunch Registry

https://tobiasrausch.com/delly/

Integrated structural variant prediction software that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout genome.

Proper citation: DELLY (RRID:SCR_004603) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/kdetrees/

R package using a non-parametric method for estimating distributions of phylogenetic trees, with the goal of identifying trees that are significantly different from the rest of the trees in the sample.

Proper citation: Kdetrees (RRID:SCR_004522) Copy   

•   Source: SciCrunch Registry

http://www.niehs.nih.gov/research/resources/software/biostatistics/eagleview/

An information-rich viewer for next-generation genome assembles with data integration capability. EagleView can display a dozen different types of information including base qualities, machine specific trace signals, and genome feature annotations. It provides an easy way for inspecting visually the quality of a genome assembly and validating polymorphism candidate sites (e.g., SNPs) reported by polymorphism discovery tools. It can also facilitate data interpretation and hypothesis generation. EagleView is a multi-platform application developed with C++ and is available for all three major platforms: Windows, Linux, and Mac OS.

Proper citation: EagleView (RRID:SCR_006859) 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://bioconductor.org/packages/2.12/bioc/html/seqbias.html

Software package that implements a model of per-position sequencing bias in high-throughput sequencing data using a simple Bayesian network, the structure and parameters of which are trained on a set of aligned reads and a reference genome sequence.

Proper citation: seqbias (RRID:SCR_006832) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/edmr/

Comprehensive differentially methylated regions (DMR) analysis based on bimodal normal distribution model and weighted cost function for regional methylation analysis optimization.

Proper citation: eDMR (RRID:SCR_006960) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/devel/bioc/html/MethylAid.html

Software for visual and interactive quality control of large Illumina 450k data sets. Bad quality samples are detected using sample-dependent and sample-independent controls present on the array and user adjustable thresholds. In depth exploration of bad quality samples can be performed using several interactive diagnostic plots of the quality control probes present on the array. Furthermore, the impact of any batch effect provided by the user can be explored.

Proper citation: MethylAid (RRID:SCR_002659) Copy   

•   Source: SciCrunch Registry

http://kirchnerlab.github.io/libmgf/

A flex/bison-based C++ Mascot Generic Format (MGF) parser library.

Proper citation: libmgf (RRID:SCR_002664) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/ExomeDepth/

Software that calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.

Proper citation: ExomeDepth (RRID:SCR_002663) Copy   

•   Source: SciCrunch Registry

https://github.com/rcanovas/libCSAM

Contains several C++ codes for compress, decompress, and access each of the fields of any SAM format file.

Proper citation: libCSAM (RRID:SCR_002766) Copy   

•   Source: SciCrunch Registry

https://github.com/lh3/ropebwt2

A software tool for constructing the FM-index for a collection of DNA sequences. It works by incrementally inserting one or multiple sequences into an existing pseudo-BWT position by position, starting from the end of the sequences. This algorithm can be largely considered a mixture of BCR and dynamic FM-index. Nonetheless, ropeBWT2 is unique in that it may implicitly sort the input into reverse lexicographical order (RLO) or reverse-complement lexicographical order (RCLO) while building the index.

Proper citation: RopeBWT2 (RRID:SCR_002673) Copy   

•   Source: SciCrunch Registry

https://github.com/ahmohamed/NetPathMiner

Software that implements a flexible module-based process flow for network path mining and visualization, which can be fully inte-grated with user-customized functions. It supports construction of various types of genome scale networks from three different pathway file formats (KGML, SBML and BioPAX), enabling its utility to most common pathway databases. In addition, it provides different visualization techniques to facilitate the analysis of even thousands of output paths.

Proper citation: NetPathMiner (RRID:SCR_002757) Copy   

•   Source: SciCrunch Registry

http://yu68.github.io/GATE/

Model-based, open source software analysis tool for chromatin states prediction based on time-course epigenetic marks data. It uses a combinatory Finite Mixture model nested with HMM to model the time course marks data in which each single hidden markov model describes the hidden states for a region set across different time points.

Proper citation: GATE (RRID:SCR_002756) Copy   

•   Source: SciCrunch Registry