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https://esp.gs.washington.edu/
Project focused on understanding the contribution of rare genetic variation to heart, lung and blood disorders through the sequencing of well-phenotyped populations.
Proper citation: NHLBI Grand Opportunity Exome Sequencing Project (RRID:SCR_010798) Copy
http://mirspring.victorchang.edu.au/
Pipeline scripts for creating a miRspring (miRNA sequence profiling) document, a new way of sharing and analysing sequencing data for small RNA.
Proper citation: miRspring (RRID:SCR_010832) Copy
http://sites.psu.edu/axtell/software/shortstack/
A software tool developed to process and analyze small RNA-seq data with respect to a reference genome, and output a comprehensive and informative annotation of all discovered small RNA genes. ShortStack discovers small RNA ''clusters'' de novo, based on user-set thresholds, and annotates clusters with respect to small RNA size, orientation, and repetitiveness. ShortStack also discovers and annotates MIRNA genes, and other Hairpin-associated small RNA genes. In addition, ShortStack includes a robust method to detect genes producing small RNAs in a phased manner. It outputs a descriptive table of all results, useful genome browser tracks, a table describing the results of the hairpin / MIRNA analysis for each cluster, and detailed text-based alignments of all MIRNAs and hairpin-associated clusters. It can also be run in ''count'' mode, to quantify a set of input loci with genomic coordinates determined a priori by the user. ShortStack is a perl program. Besides perl, ShortStack also requires samtools and the RNALfold and RNAeval programs from the Vienna RNA Package to execute. When used to control the alignment of small RNA data to a reference genome, ShortStack also requires bowtie and bowtie-build. Finally, for optimal results, ShortStack uses a file of inverted repeats produced by the EMBOSS application einverted.
Proper citation: ShortStack (RRID:SCR_010834) Copy
https://code.google.com/p/reseqtools/
A Toolkit for analyzing next-generation DNA Re-Sequencing data.
Proper citation: reseqtools (RRID:SCR_010806) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18,2023. Targeted RE-sequencing Annotation Tool that offers a comprehensive, open framework, end-to-end solution for analyzing and interpreting targeted re-sequencing data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: TREAT (RRID:SCR_010808) Copy
Software that identifies and annotates mutations in next-generation sequencing projects.
Proper citation: GAMES (RRID:SCR_010762) Copy
http://genome.sph.umich.edu/wiki/GlfMultiples
A GLF-based variant caller for next-generation sequencing data.
Proper citation: glfMultiples (RRID:SCR_010763) Copy
http://www.ufpel.tche.br/faem/fitotecnia/fitomelhoramento/faleconosco.html
A software tool for detection and characterization of micro- and minisatellites in DNA sequences.
Proper citation: SSRLocator (RRID:SCR_010766) Copy
Software for the Identification of Microsatellite Sequences from Paired-End Illumina High-Throughput DNA Sequence Data
Proper citation: SSR pipeline (RRID:SCR_010767) Copy
https://code.google.com/p/draw-sneakpeek/
Analysis Workflow and Quality Metric Management for DNA-Seq Experiments.
Proper citation: draw-sneakpeek (RRID:SCR_010801) Copy
http://trhist.gi.k.u-tokyo.ac.jp/
A software tool for finding significant tandem repeats using short reads.
Proper citation: TRhist (RRID:SCR_010769) Copy
http://www.compbio.group.cam.ac.uk/software/cnaseg/
A novel framework for the identification of CNA events that uses flowcell-to-flowcell variability to estimate the false positive rate and the depth of coverage to finalize copy number calls.
Proper citation: CNAseg (RRID:SCR_010817) Copy
http://www.sanger.ac.uk/resources/software/cnd/
A program to detect copy number variants from short read sequence data.
Proper citation: CnD (RRID:SCR_010818) Copy
http://mendel.stanford.edu/SidowLab/downloads/MAPP/
Java program that predicts the impact of all possible amino acid substitutions on the function of the protein., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: MAPP (RRID:SCR_010775) Copy
http://www.ngsbicocca.org/html/ceqer.html
A graphical, event-driven tool for CNA/AI-coupled analysis of exome sequencing reads.
Proper citation: CEQer (RRID:SCR_010813) Copy
http://bg.upf.edu/group/projects/oncodrive-fm.php
An approach to uncover driver genes or gene modules.
Proper citation: Oncodrive-fm (RRID:SCR_010781) Copy
https://sites.google.com/site/vibansal/software/crisp
A software program to detect SNPs and short indels from pooled sequencing data generated using next-generation sequencing instruments.
Proper citation: CRISP (RRID:SCR_010759) Copy
https://github.com/ice91/CloudBrush
A De Novo Next Generation Genomic Sequence Assembler Based on String Graph and MapReduce Cloud Computing Framework.
Proper citation: CloudBrush (RRID:SCR_010751) Copy
http://www.bcgsc.ca/platform/bioinfo/software/ssake
Software designed to help leverage the information from short sequences reads by stringently clustering them into contigs that can be used to characterize novel sequencing targets.
Proper citation: SSAKE (RRID:SCR_010753) Copy
https://code.google.com/p/comb/
A software package designed for the downstream analysis of short read mapping data produced by the ABI SOLiD and Illumina sequencing platforms.
Proper citation: ComB (RRID:SCR_010757) Copy
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