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http://www.broadinstitute.org/software/cprg/?q=node/39
An algorithm to identify chromosomal breakpoints using massively parallel next generation sequence data.
Proper citation: SegSeq (RRID:SCR_010826) Copy
Offers the researchers an automatic pipeline to predict the disease-association of SAPs.
Proper citation: SAPRED (RRID:SCR_010785) Copy
http://seqanswers.com/wiki/JointSLM
Copy number estimation from read depth information.
Proper citation: JointSLM (RRID:SCR_010823) Copy
http://genetics.cs.ucla.edu/eminim/
A software tool for imputation of unobserved genotypes using a set of reference haplotype panel at a higher-density SNP set such as HapMap, and lower-density genotypes of a target individual using such as genotyping arrays.
Proper citation: EMINIM (RRID:SCR_010790) Copy
http://genetics.cs.ucla.edu/harsh/
Software that provides a method to infer the haplotype using haplotype reference panel and high throughput sequencing data.
Proper citation: HARSH (RRID:SCR_010792) Copy
http://www.bioinf.jku.at/research/short-IBD/
Software that identifies short identity by descent (IBD) segments that are tagged by rare variants in large sequencing data.
Proper citation: HapFABIA (RRID:SCR_010793) Copy
http://www3a.biotec.or.th/c-mii/
A software tool for plant miRNA and target identification. C-mii pipelines are based on combined steps and criteria from previous studies and also incorporated with several tools such as standalone BLAST and UNAFold and pre-installed databases including miRBase, UniProt, and Rfam. C-mii provides following distinguished features. First, it comes with graphical user interfaces of well-defined pipelines for both miRNA and target identifications with reliable results. Second, it provides a set of filters allowing users to reduce the number of results corresponding to the recently proposed constraints in plant miRNA and target biogenesis. Third, it extends the standard computational steps of miRNA target identification with miRNA-target folding module and GO annotation. Fourth, it supplies the bird eye views of the identification results with info-graphics and grouping information. Fifth, it provides helper functions for database update and auto-recovery to ease system usage and maintenance. Finally, it supports the multi-project and multi-thread management to improve the computational speed.
Proper citation: C-mii (RRID:SCR_010839) Copy
http://www.wageningenur.nl/en/show/Pedimap.htm
A software tool for visualizing phenotypic and genotypic data for related individuals linked in pedigrees.
Proper citation: Pedimap (RRID:SCR_010796) Copy
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
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