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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
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
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
http://snoopcgh.sourceforge.net/
A java desktop application for visualising and exploring comparative genomic hybridization (CGH) data.
Proper citation: SnoopCGH (RRID:SCR_004420) Copy
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
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
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
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
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
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
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
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
http://ibis.tau.ac.il/miRNAkey/
A software pipeline for the analysis of microRNA Deep Sequencing data.
Proper citation: miRNAKey (RRID:SCR_004813) Copy
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
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
http://mrsfast.sourceforge.net/
A cache-oblivious algorithm designed to map short reads to reference genome assemblies in a fast and memory-efficient manner. It optimizes cache usage to get higher performance. Currently Supported Features: * Mistmatches, No indels * Paired-end Mapping Mode * Discordant Paired-end Mapping Mode (to be used in conjuction with Variation Hunter)
Proper citation: mrsFAST (RRID:SCR_003128) Copy
http://acgt.cs.tau.ac.il/hyden/
Software program for designing pairs of degenerate primers for a given set of DNA sequences. It works well for large input sets of genomic sequences (e.g., hundreds of sequences of length 1Kbp). It is a batch (i.e., command-line, as opposed to graphical interface) program, available for Windows XP (downloadable version) and Linux (upon request).
Proper citation: HYDEN (RRID:SCR_003126) Copy
http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html
Software package for quantitative DNA sequencing for chromosomal aberrations providing a robust, cost-effective WGS method for DNA copy number analysis. The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.
Proper citation: QDNAseq (RRID:SCR_003174) Copy
https://github.com/hangelwen/miR-PREFeR
An accurate, fast, and easy-to-use plant miRNA prediction software tool using small RNA-Seq data. It utilizes expression patterns of miRNA and follows the criteria for plant microRNA annotation to accurately predict plant miRNAs from one or more small RNA-Seq data samples of the same species.
Proper citation: miR-PREFeR (RRID:SCR_003353) Copy
An algorithm for the identification of microRNA targets. Details are provided (3' UTR alignments with predicted sites, links to various public databases etc) regarding: # microRNA target predictions in vertebrates (Krek et al, Nature Genetics 37:495-500 (2005)) # microRNA target predictions in seven Drosophila species (Grn et al, PLoS Comp. Biol. 1:e13 (2005)) # microRNA targets in three nematode species (Lall et al, Current Biology 16, 1-12 (2006)) # human microRNA targets that are not conserved but co-expressed (i.e. the microRNA and mRNA are expressed in the same tissue) (Chen and Rajewsky, Nat Genet 38, 1452-1456 (2006)) co-expressed targets
Proper citation: PicTar (RRID:SCR_003343) Copy
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