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http://www.clipz.unibas.ch/downloads/TSSer/index.php

A computational pipeline to analyze differential RNA sequencing (dRNA-seq) data to determine transcription start sites genome-wide.

Proper citation: TSSer (RRID:SCR_006419) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/cohcap/

An algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). It provides QC metrics, differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, and visualization of methylation values.

Proper citation: COHCAP (RRID:SCR_006499) Copy   

•   Source: SciCrunch Registry

http://sammeth.net/confluence/display/FLUX/Home

Software to recontruct abundances of known transcript forms from RNAseq data. The algorithm works by distributing the reads mapping to a given exonic region (or splice junction) among the transcripts including the exon (or splice junction). The input is the annotation of a reference transcriptome and reads from RNAseq technologies aligned to the genome. From the reference annotation, splicing graphs are produced and reads are mapped to corresponding edges in these graphs according to the position where they align in the genomic sequence. The resulting graph with edges labelled by the number of reads can be interpreted as a flow network where each transcript representing a transportation path from its start to its end and consequently each edge a possibly shared segment of transportation along which a certain number of reads per nucleotide -- i.e., a flux -- is observed. Given a density function of reads along a transcript, the expected participation of each transcript in an edge under consideration can be estimated. The basic idea is to cast back from these latter participations and the observed number of reads - allowing for a certain amount of noise - to the original transcript abundancies. To do so, a linear constraint is formalized for each edge, and an optimal solution for the complete set of constraints is found by a standard linear program solver.

Proper citation: FLUX CAPACITOR (RRID:SCR_006651) 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://omics.pnl.gov/software/ms-gf

Software that performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.

Proper citation: MS-GF+ (RRID:SCR_015646) 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

http://utgenome.org/index.html

An open-source software for developing personalized genome browsers that work in web browsers.

Proper citation: UTGB Toolkit (RRID:SCR_011797) Copy   

•   Source: SciCrunch Registry

http://graphics.med.yale.edu/trim/

A fast and lightweight software to trim adapters and low quality regions in reads from ultra high-throughput next-generation sequencing machines.

Proper citation: Btrim (RRID:SCR_011836) Copy   

•   Source: SciCrunch Registry

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

Software tool that removes adapter sequences from DNA sequencing reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: cutadapt (RRID:SCR_011841) Copy   

•   Source: SciCrunch Registry

http://genopole.pasteur.fr/SynTView/

An interactive multi-view genome browser for next-generation comparative microorganism genomics.

Proper citation: SynTView (RRID:SCR_011939) Copy   

•   Source: SciCrunch Registry

http://cbb.sjtu.edu.cn/~ccwei/pub/software/NeSSM.php

A Next-Generation Sequencing Simulator for Metagenomics.

Proper citation: NeSSM (RRID:SCR_011941) Copy   

•   Source: SciCrunch Registry

http://metavelvet.dna.bio.keio.ac.jp/

Software for a short read de novo metagenome assembly created by modifying and extending a single-genome and de Bruijn-graph based assembler, Velvet.

Proper citation: MetaVelvet (RRID:SCR_011915) Copy   

•   Source: SciCrunch Registry

http://omics.informatics.indiana.edu/GeneStitch/

Network Matching Algorithm using the de Bruijn graph assembly of metagenomes to improve the assembly of genes.

Proper citation: GeneStitch (RRID:SCR_011910) Copy   

•   Source: SciCrunch Registry

http://bayescall.sourceforge.net/

An efficient model-based base-calling algorithm for high-throughput sequencing.

Proper citation: naiveBayesCall (RRID:SCR_011866) Copy   

•   Source: SciCrunch Registry

http://pages.cs.wisc.edu/~bsettles/abner/

A software tool for molecular biology text analysis. At ABNER''s core is a statistical machine learning system using linear-chain conditional random fields (CRFs) with a variety of orthographic and contextual features.

Proper citation: ABNER (RRID:SCR_011868) Copy   

•   Source: SciCrunch Registry

http://transcriptome.ens.fr/eoulsan/

A versatile framework based on the Hadoop implementation of the MapReduce algorithm, dedicated to high throughput sequencing data analysis on distributed computers.

Proper citation: Eoulsan (RRID:SCR_011901) Copy   

•   Source: SciCrunch Registry