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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.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml

Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI''s Entrez retrieval service. Cn3D runs on Windows, Macintosh, and Unix. Cn3D simultaneously displays structure, sequence, and alignment, and now has powerful annotation and alignment editing features. Cn3D is a tool for visualization of three-dimensional structures with emphasis on interactive examination of sequence-structure relationships and superposition of geometrically similar structures. Can be used to display MMDB structures, superpositions of VAST related structures, and conserved core motifs identified in conserved domains.

Proper citation: NCBI Structure: Cn3D (RRID:SCR_004861) Copy   

•   Source: SciCrunch Registry

http://metaphyler.cbcb.umd.edu/

A taxonomic classifier for metagenomic shotgun reads, which uses phylogenetic marker genes as a taxonomic reference. The classifier, based on BLAST, uses different thresholds (automatically learned from the reference database) for each combination of taxonomic rank, reference gene, and sequence length. The reference database includes marker genes from all complete genomes, several draft genomes and the NCBI nr protein database.

Proper citation: MetaPhyler (RRID:SCR_004848) Copy   

•   Source: SciCrunch Registry

http://hyfi.sourceforge.net/

This collection of software is designed to rapidly identify identifies primer and microarray probe binding sites for a query sequence in genomic DNA. This software suite has four main programs:1. A program for indexing a sequence file to speed up the binding site search. 2. A program for retrieving the binding sites of a query sequence. 3. A program for identifying sites where PCR primers could co-operate to exponentially amplify a sequence 4. A program for analyzing a set of binding sites to tailor the search for different reaction conditions. This software is implemented in C.

Proper citation: hyfi: software suite for binding site search (RRID:SCR_004884) Copy   

•   Source: SciCrunch Registry

http://useq.sourceforge.net/

A collection of software tools for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms.

Proper citation: USeq (RRID:SCR_004753) Copy   

•   Source: SciCrunch Registry

http://ibis.tau.ac.il/miRNAkey/

A software pipeline for the analysis of microRNA Deep Sequencing data.

Proper citation: miRNAKey (RRID:SCR_004813) Copy   

•   Source: SciCrunch Registry

http://svmerge.sourceforge.net/

Software pipeline to detect structural variants (SVs) by integrating calls from several existing SV callers, which are then validated and the breakpoints refined using local de novo assembly. The output is in BED format allowing for easy downstream analysis or viewing in a genome browser. It is modular and extensible allowing new callers to be incorporated as they become available.

Proper citation: SVMerge (RRID:SCR_004777) Copy   

•   Source: SciCrunch Registry

http://www.engr.uconn.edu/~jiz08001/svseq2.html

Software for accurate and efficient calling of structural variations with low-coverage sequence data. Version 2 uses the BAM files of paired Illumina reads with soft-clip signature as input. It calls both deletions and insertions.

Proper citation: SVseq (RRID:SCR_004804) Copy   

•   Source: SciCrunch Registry

http://minia.genouest.org/

A short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.

Proper citation: Minia (RRID:SCR_004986) Copy   

•   Source: SciCrunch Registry

http://www.cs.helsinki.fi/u/lmsalmel/mip-scaffolder/

A software program for scaffolding contigs produced by fragment assemblers using mate pair data such as those generated by ABI SOLiD or Illumina Genome Analyzer.

Proper citation: MIP Scaffolder (RRID:SCR_005072) Copy   

•   Source: SciCrunch Registry

http://zhanglab.c2b2.columbia.edu/index.php/OLego

A program specifically designed for de novo spliced mapping of mRNA-seq reads. It adopts a multiple-seed-and-extend scheme, and does not rely on a separate external mapper.

Proper citation: OLego (RRID:SCR_005811) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/pepr-chip-seq/

A ChIP-Seq peak calling or differential binding analysis tool that is primarily designed for data with biological replicates. It uses a negative binomial distribution to model the read counts among the samples in the same group, and look for consistent differences between ChIP and control group or two ChIP groups run under different conditions.

Proper citation: PePr (RRID:SCR_005759) Copy   

•   Source: SciCrunch Registry