Tools   Select Another Resource Report Type

http://samstat.sourceforge.net/

C software program for displaying sequence statistics for next generation sequencing. Works with large fasta, fastq and SAM/BAM files.

Proper citation: SAMStat (RRID:SCR_005432) Copy   

•   Source: SciCrunch Registry

http://dna.leeds.ac.uk/methylviewer/

A simple integrated software tool for handling MAP (methyltransferase accessibility protocol) and MAP-IT (MAP individual templates) footprinting projects. It can process sequence data (*.txt, *.ab1 and *.scf) derived from the use of up to four different DNA methyltransferases.

Proper citation: MethylViewer (RRID:SCR_005448) Copy   

•   Source: SciCrunch Registry

http://epigenome.usc.edu/publicationdata/bissnp2011/

A software package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping and accurate DNA methylation calling in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq, RRBS and any other bisulfite treated sequencing) with Illumina directional library protocol. It contains the following key features: * Call and summarize methylation of any cytosine context provided (CpG, CHH, CHG, GCH et.al.); * Work for single end and paired-end data; * Accurtae variant detection. Enable base quality recalibration and indel calling in bisulfite sequencing; * Based on Java map-reduce framework, allow multi-thread computing. Cross-platform; * Allow multiple output format, detailed VCF files, CpG haplotype reads file for mono-allelic methylation analysis, simplified bedGraph, wig and bed format for visualization in UCSC genome broswer and IGV browser. BisSNP uses bayesian inference with locus specific methylation probabilities and bisulfite conversion rate of different cytosine context(not only CpG, CHH, CHG in Bisulfite-seq, but also GCH et.al. in other bisulfite treated sequencing) to determine genotypes and methylation levels simultaneously., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Bis-SNP (RRID:SCR_005439) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/distmap/

A user-friendly software pipeline designed to map short reads in a MapReduce framework on a local Hadoop cluster. It is designed to be easily implemented by researchers who do not have expert knowledge of bioinformatics. As it does not have any dependencies, it provides full flexibility and control to the user. The user can use any version of a compatible mapper and any reference genome assembly. There is no need to maintain the mapper, reference or DistMap source code on each of the slaves (nodes) in the Hadoop cluster, making maintenance extremely easy.

Proper citation: DistMap (RRID:SCR_005473) Copy   

•   Source: SciCrunch Registry

http://www.well.ox.ac.uk/project-stampy

A software package for the mapping of short reads from illumina sequencing machines onto a reference genome. It''s recommended for most workflows, including those for genomic resequencing, RNA-Seq and Chip-seq. Stampy excels in the mapping of reads containing that contain sequence variation relative to the reference, in particular for those containing insertions or deletions. It can map reads from a highly divergent species to a reference genome for instance. Stampy achieves high sensitivity and speed by using a fast hashing algorithm and a detailed statistical model. Stampy has the following features: * Maps single, paired-end and mate pair Illumina reads to a reference genome * Fast: about 20 Gbase per hour in hybrid mode (using BWA) * Low memory footprint: 2.7 Gb shared memory for a 3Gbase genome * High sensitivity for indels and divergent reads, up to 10-15% * Low mapping bias for reads with SNPs * Well calibrated mapping quality scores * Input: Fastq and Fasta; gzipped or plain * Output: SAM, Maq''s map file * Optionally calculates per-base alignment posteriors * Optionally processes part of the input * Handles reads of up to 4500 bases

Proper citation: Stampy (RRID:SCR_005504) Copy   

•   Source: SciCrunch Registry

http://ngsview.sourceforge.net/

A generally applicable, flexible and extensible next-generation sequence alignment editor. The software allows for visualization and manipulation of millions of sequences simultaneously on a desktop computer, through a graphical interface.

Proper citation: NGSView (RRID:SCR_005637) Copy   

•   Source: SciCrunch Registry

http://www.bioinformatics.babraham.ac.uk/projects/hicup/

A tool for mapping and performing quality control on Hi-C data.

Proper citation: HiCUP (RRID:SCR_005569) Copy   

•   Source: SciCrunch Registry

http://cbil.upenn.edu/RUM/

An alignment, junction calling, and feature quantification pipeline specifically designed for Illumina RNA-Seq data.

Proper citation: RUM (RRID:SCR_008818) Copy   

•   Source: SciCrunch Registry

https://github.com/armintoepfer/QuasiRecomb/releases

A jumping hidden Markov model that describes the generation of the viral quasispecies and a method to infer its parameters by analysing next generation sequencing data.

Proper citation: QuasiRecomb (RRID:SCR_008812) Copy   

•   Source: SciCrunch Registry

https://genome.unc.edu/xpn/

Merging Two Gene Expression Studies via Cross Platform Normalization.

Proper citation: XPN (RRID:SCR_008845) Copy   

•   Source: SciCrunch Registry

http://tvap.genome.wustl.edu/tools/music/

A set of tools aimed at determining the significance of somatic mutations discovered within a given cohort of cancer samples, incorporating the cohort''s alignment data, variant lists and any relevant clinical data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MuSiC (RRID:SCR_008792) Copy   

•   Source: SciCrunch Registry

https://gemini.readthedocs.io/en/latest/

Framework for exploring genetic variation in the context of the genome annotations available for the human genome. Users can load a VCF file into a database and each variant is automatically annotated by comparing it to several genome annotations from source such as ENCODE tracks, UCSC tracks, OMIM, dbSNP, KEGG, and HPRD.

Proper citation: GEMINI (RRID:SCR_014819) 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

https://github.com/steinmann/peakzilla

An algorithm to identify transcription factor binding sites from ChIP-seq data.

Proper citation: Peakzilla (RRID:SCR_007471) Copy   

•   Source: SciCrunch Registry

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

A collection of programs for the removal of noise from 454 sequenced PCR amplicons. This project also includes the Perseus algorithm for chimera removal.

Proper citation: AmpliconNoise (RRID:SCR_007814) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/Tools/msa/kalign/

A fast and accurate multiple sequence alignment algorithm.

Proper citation: Kalign (RRID:SCR_011810) Copy   

•   Source: SciCrunch Registry

http://wishart.biology.ualberta.ca/cgview/

A Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CGView (RRID:SCR_011779) Copy   

•   Source: SciCrunch Registry

http://bioen-compbio.bioen.illinois.edu/PSAR-Align/

Software for improving multiple sequence alignment using probabilistic sampling.

Proper citation: PSAR-Align (RRID:SCR_011814) Copy   

•   Source: SciCrunch Registry

http://gaggle.systemsbiology.net/docs/geese/genomebrowser/

An open source software tool for visualizing high-density data plotted against coordinates on the genome.

Proper citation: Gaggle (RRID:SCR_011780) Copy   

•   Source: SciCrunch Registry

https://bioinf.eva.mpg.de/patman/

Software that searches for short patterns in large DNA databases, allowing for approximate matches., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PatMaN (RRID:SCR_011821) Copy   

•   Source: SciCrunch Registry