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http://www.ncbi.nlm.nih.gov/sra

Repository of raw sequencing data from next generation of sequencing platforms including including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helicos Heliscope, Complete Genomics, and Pacific Biosciences SMRT. In addition to raw sequence data, SRA now stores alignment information in form of read placements on reference sequence. Data submissions are welcome. Archive of high throughput sequencing data,part of international partnership of archives (INSDC) at NCBI, European Bioinformatics Institute and DNA Database of Japan. Data submitted to any of this three organizations are shared among them.

Proper citation: NCBI Sequence Read Archive (SRA) (RRID:SCR_004891) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.rutgers.edu/Software/SLiQ/

Software for simple linear inequalities based Mate-Pair reads filtering and scaffolding. A set of simple linear inequalities (SLIQ) derived from the geometry of contigs on the line that can be used to predict the relative positions and orientations of contigs from individual mate pair reads and thus produce a contig digraph. The SLIQ inequalities can also filter out unreliable mate pairs and can be used as a pre-processing step for any scaffolding algorithm. This tool filters mate pairs and then produces a Directed Contig Graph (contig diGraph). Also provided is a Naive scaffolder that can then produce scaffolds out of the contig diGraph.

Proper citation: SLIQ (RRID:SCR_005003) Copy   

•   Source: SciCrunch Registry

http://cortexassembler.sourceforge.net/index_cortex_var.html

A tool for genome assembly and variation analysis from sequence data. You can use it to discover and genotype variants on single or multiple haploid or diploid samples. If you have multiple samples, you can use Cortex to look specifically for variants that distinguish one set of samples (eg phenotype=X, cases, parents, tumour) from another set of samples (eg phenotype=Y, controls, child, normal). cortex_var features * Variant discovery by de novo assembly - no reference genome required * Supports multicoloured de Bruijn graphs - have multiple samples loaded into the same graph in different colours, and find variants that distinguish them. * Capable of calling SNPs, indels, inversions, complex variants, small haplotypes * Extremely accurate variant calling - see our paper for base-pair-resolution validation of entire alleles (rather than just breakpoints) of SNPs, indels and complex variants by comparison with fully sequenced (and finished) fosmids - a level of validation beyond that demanded of any other variant caller we are aware of - currently cortex_var is the most accurate variant caller for indels and complex variants. * Capable of aligning a reference genome to a graph and using that to call variants * Support for comparing cases/controls or phenotyped strains * Typical memory use: 1 high coverage human in under 80Gb of RAM, 1000 yeasts in under 64Gb RAM, 10 humans in under 256 Gb RAM

Proper citation: cortex var (RRID:SCR_005081) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/ega/

Web service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The repository allows you to explore datasets from numerous genotype experiments, supplied by a range of data providers. The EGA''s role is to provide secure access to the data that otherwise could not be distributed to the research community. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. As an example, only members of the EGA team are allowed to process data in a secure computing facility. Once processed, all data are encrypted for dissemination and the encryption keys are delivered offline. The EGA also supports data access only for the consortium members prior to publication.

Proper citation: European Genome phenome Archive (RRID:SCR_004944) Copy   

•   Source: SciCrunch Registry

http://www.physics.rutgers.edu/~anirvans/SOPRA/

Software tool to exploit the mate pair/paired-end information for assembly of short reads from high throughput sequencing platforms, e.g. Illumina and SOLiD.

Proper citation: SOPRA (RRID:SCR_005035) Copy   

•   Source: SciCrunch Registry

http://www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformatics-solutions/sspacev12/

A stand-alone software program for scaffolding pre-assembled contigs using paired-read data. Main features are: a short runtime, multiple library input of paired-end and/or mate pair datasets and possible contig extension with unmapped sequence reads.

Proper citation: SSPACE (RRID:SCR_005056) Copy   

•   Source: SciCrunch Registry

http://meringlab.org/software/hpc-clust/

A set of tools designed to cluster large numbers (>1 million) of pre-aligned nucleotide sequences. It performs the clustering of sequences using the Hierarchical Clustering Algorithm (HCA). There are currently three different cluster metrics implemented: single-linkage, complete-linkage, and average-linkage. In addition, there are currently four sequence distance functions implemented, these are: identity (gap-gap counting as match), nogap (gap-gap being ignored), nogap-single (like nogap, but consecutive gap-nogap''s count as a single mismatch), tamura (distance is calculated with the knowledge that transitions are more likely than transversions). One advantage that HCA has over other algorithms is that instead of producing only the clustering at a given threshold, it produces the set of merges occuring at each threshold. With this approach, the clusters can afterwards very quickly be reported for every arbitrary threshold with little extra computation. This approach also allows the plotting of the variation of number of clusters with clustering threshold without requiring the clustering to be run for each threshold independently. Another feature of the way HPC-CLUST is implemented is that the single-, complete-, and average-linkage clusterings can be computed in a single run with little overhead.

Proper citation: HPC-CLUST (RRID:SCR_005052) Copy   

•   Source: SciCrunch Registry

http://plaza.ufl.edu/xywang/Mpick.htm

A modularity-based clustering software for Operational Taxonomic Unit (OTU) picking of 16S rRNA sequences. The algorithm does not require a predetermined cut-off level, and our simulation studies suggest that it is superior to existing methods that require specified distance or variance levels to define OTUs.

Proper citation: M-pick (RRID:SCR_004995) Copy   

•   Source: SciCrunch Registry

http://plaza.ufl.edu/sunyijun/ES-Tree.htm

Software for hierarchical Clustering Analysis of Millions of 16S rRNA Pyrosequences in Quasi-linear Time.

Proper citation: ESPRIT-Tree (RRID:SCR_005045) Copy   

•   Source: SciCrunch Registry

http://www.geneontology.org/

Computable knowledge regarding functions of genes and gene products. GO resources include biomedical ontologies that cover molecular domains of all life forms as well as extensive compilations of gene product annotations to these ontologies that provide largely species-neutral, comprehensive statements about what gene products do. Used to standardize representation of gene and gene product attributes across species and databases.

Proper citation: Gene Ontology (RRID:SCR_002811) Copy   

•   Source: SciCrunch Registry

http://biohealth.snu.ac.kr/software/TRAP/

A comprehensive software package integrating all necessary tasks such as mapping short reads, measuring gene expression levels, finding differentially expressed genes (DEGs), clustering and pathway analysis for time-series data in a single environment.

Proper citation: Time-series RNA-seq Analysis Package (RRID:SCR_002935) Copy   

•   Source: SciCrunch Registry

http://pfind.ict.ac.cn/software/pBuild/index.html

A software tool that can compare several search engines' results and combine them together.

Proper citation: pBuild (RRID:SCR_002929) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/src/contrib/Archive/aCGH.Spline/

An R package for array comparative genomic hybridization (aCGH) dye bias normalization.

Proper citation: aCGH.Spline (RRID:SCR_002927) Copy   

•   Source: SciCrunch Registry

https://github.com/GiBacci/StreamingTrim/

A DNA reads trimming software, written in Java, with which researchers are able to analyse the quality of DNA sequences in fastq files and to search for low-quality zones in a very conservative way.

Proper citation: StreamingTrim (RRID:SCR_002922) Copy   

•   Source: SciCrunch Registry

http://pfind.ict.ac.cn/software/pLabel/index.html

Mass spectral peak labeling software developed for proteomics research., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: pLabel (RRID:SCR_002923) Copy   

•   Source: SciCrunch Registry

https://github.com/itojal/hot_scan

A free software to detect genomic regions unusually rich in translocation breakpoints. More generally, it may be used to detect a region that is unusually rich in a given character of a binary sequence.

Proper citation: hot scan (RRID:SCR_002840) Copy   

•   Source: SciCrunch Registry

http://rdock.sourceforge.net/

A fast and versatile Open Source docking software program that can be used to dock small molecules against proteins and nucleic acids.

Proper citation: rDock (RRID:SCR_002838) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/Basic4Cseq.html

An R/Bioconductor package for basic filtering, analysis and subsequent near-cis visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment's viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile.

Proper citation: Basic4Cseq (RRID:SCR_002836) Copy   

•   Source: SciCrunch Registry

https://github.com/PacificBiosciences/SMRT-Analysis/

Open-source bioinformatics software suite for analyzing single molecule, real-time DNA sequencing data. Users can choose from a variety of analysis protocols that utilize PacBio and third-party tools. Analysis protocols include de novo genome assembly, cDNA mapping, DNA base-modification detection, and long-amplicon analysis to determine phased consensus sequences.

Proper citation: SMRT-Analysis (RRID:SCR_002942) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/mzR.html

Software that provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a wrapper for the ISB random access parser for mass spectrometry mzXML, mzData and mzML files.

Proper citation: mzR (RRID:SCR_002856) Copy   

•   Source: SciCrunch Registry