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http://www.cibiv.at/~niko/ngc/

A compressor for aligned HTS sequencing data that enables the complete lossless and lossy compression of mapped alignment data stored in SAM/BAM files.

Proper citation: NGC (RRID:SCR_009342) Copy   

•   Source: SciCrunch Registry

http://geckoe.sourceforge.net/

A complete, high-capacity centralized gene expression analysis system, developed in response to the needs of a distributed user community.

Proper citation: Gecko (RRID:SCR_009001) Copy   

•   Source: SciCrunch Registry

http://homes.cs.washington.edu/~dcjones/quip/

Compresses next-generation sequencing data in the FASTQ and SAM/BAM formats with extreme prejudice.

Proper citation: Quip (RRID:SCR_009362) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.ua.pt/software/mfcompress/

A compression tool for FASTA and multi-FASTA files.

Proper citation: MFCompress (RRID:SCR_009301) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.research.nicta.com.au/software/rlz/

Optimized relative Lempel-Ziv compression of genomes.

Proper citation: RLZ (RRID:SCR_009420) Copy   

•   Source: SciCrunch Registry

http://ftp://ftp.ieeta.pt/~ap/codecs/GReEn1.tar.gz

A compression tool recently proposed for compressing genome resequencing data using a reference genome sequence., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GReEn (RRID:SCR_009264) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/cancer/cga/indelocator

A software tool for calling short indels in next generation sequencing data.

Proper citation: Indelocator (RRID:SCR_005258) Copy   

•   Source: SciCrunch Registry

http://compbio.cs.brown.edu/projects/gasv/

Software tool combining both paired read and read depth signals into probabilistic model which can analyze multiple alignments of reads. Used to find structural variation in both normal and cancer genomes using data from variety of next-generation sequencing platforms. Used to predict structural variants directly from aligned reads in SAM/BAM format.Combines read depth information along with discordant paired read mappings into single probabilistic model two common signals of structural variation. When multiple alignments of read are given, GASVPro utilizes Markov Chain Monte Carlo procedure to sample over the space of possible alignments.

Proper citation: GASVPro (RRID:SCR_005259) Copy   

•   Source: SciCrunch Registry

http://bejerano.stanford.edu/prism/public/html/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5,2022.Tool that predicts interactions between transcription factors and their regulated genes from binding motifs. Understanding vertebrate development requires unraveling the cis-regulatory architecture of gene regulation. PRISM provides accurate genome-wide computational predictions of transcription factor binding sites for the human and mouse genomes, and integrates the predictions with GREAT to provide functional biological context. Together, accurate computational binding site prediction and GREAT produce for each transcription factor: 1. putative binding sites, 2. putative target genes, 3. putative biological roles of the transcription factor, and 4. putative cis-regulatory elements through which the factor regulates each target in each functional role., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PRISM (Stanford database) (RRID:SCR_005375) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/knime4bio/

A set of custom nodes for the KNIME (The Konstanz Information Miner) graphical workbench, for analysing next-generation sequencing (NGS) data without the requirement of programming skills.

Proper citation: Knime4Bio (RRID:SCR_005376) Copy   

•   Source: SciCrunch Registry

http://ergatis.sourceforge.net/

A web interface and scalable software system for bioinformatics workflows that is used to create, run, and monitor reusable computational analysis pipelines. It contains pre-built components for common bioinformatics analysis tasks. These components can be arranged graphically to form highly-configurable pipelines. Each analysis component supports multiple output formats, including the Bioinformatic Sequence Markup Language (BSML). The current implementation includes support for data loading into project databases following the CHADO schema, a highly normalized, community-supported schema for storage of biological annotation data. Ergatis uses the Workflow engine to process its work on a compute grid. Workflow provides an XML language and processing engine for specifying the steps of a computational pipeline. It provides detailed execution status and logging for process auditing, facilitates error recovery from point of failure, and is highly scalable with support for distributed computing environments. The XML format employed enables commands to be run serially, in parallel, and in any combination or nesting level.

Proper citation: Ergatis (RRID:SCR_005377) Copy   

•   Source: SciCrunch Registry

http://toolshed.g2.bx.psu.edu/repository/display_tool?repository_id=5d0de444b1f9ac52&tool_config=database%2Fcommunity_files%2F000%2Frepo_136%2Fcrest.xml&changeset_revision=4f6952e0af48

An algorithm for detecting genomic structural variations at base-pair resolution using next-generation sequencing data. CREST uses pieces of DNA called soft clips to find structural variations. Soft clips are the DNA segments produced during sequencing that fail to properly align to the reference genome as the sample genome is reassembled. CREST uses the soft clips to precisely identify sites of chromosomal rearrangement or where pieces of DNA are inserted or deleted.

Proper citation: CREST (RRID:SCR_005257) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/molbiolib/

A compact, portable, and extensively tested C++11 software framework and set of applications tailored to the demands of next-generation sequencing data and applicable to many other applications. It is designed to work with common file formats and data types used both in genomic analysis and general data analysis. A central relational-database-like Table class is a flexible and powerful object to intuitively represent and work with a wide variety of tabular datasets, ranging from alignment data to annotations. MolBioLib includes programs to perform a wide variety of analysis tasks such as computing read coverage, annotating genomic intervals, and novel peak calling with a wavelet algorithm. This package assumes fluency in both UNIX and C++.

Proper citation: MolBioLib (RRID:SCR_005372) Copy   

•   Source: SciCrunch Registry

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

An interactive software program that integrates phenotypic data exploration, selection, management and quality control using a unified platform for association studies of rare and common variants.

Proper citation: PhenoMan (RRID:SCR_005249) Copy   

•   Source: SciCrunch Registry

http://www.bioextract.org/GuestLogin

An open, web-based system designed to aid researchers in the analysis of genomic data by providing a platform for the creation of bioinformatic workflows. Scientific workflows are created within the system by recording tasks performed by the user. These tasks may include querying multiple, distributed data sources, saving query results as searchable data extracts, and executing local and web-accessible analytic tools. The series of recorded tasks can then be saved as a reproducible, sharable workflow available for subsequent execution with the original or modified inputs and parameter settings. Integrated data resources include interfaces to the National Center for Biotechnology Information (NCBI) nucleotide and protein databases, the European Molecular Biology Laboratory (EMBL-Bank) non-redundant nucleotide database, the Universal Protein Resource (UniProt), and the UniProt Reference Clusters (UniRef) database. The system offers access to numerous preinstalled, curated analytic tools and also provides researchers with the option of selecting computational tools from a large list of web services including the European Molecular Biology Open Software Suite (EMBOSS), BioMoby, and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The system further allows users to integrate local command line tools residing on their own computers through a client-side Java applet.

Proper citation: BioExtract (RRID:SCR_005397) Copy   

•   Source: SciCrunch Registry

http://statgenpro.psychiatry.hku.hk/limx/kggseq/

A biological Knowledge-based mining platform for Genomic and Genetic studies using Sequence data. The software platform, constituted of bioinformatics and statistical genetics functions, makes use of valuable biologic resources and knowledge for sequencing-based genetic mapping of variants / genes responsible for human diseases / traits. It facilitates geneticists to fish for the genetic determinants of human diseases / traits in the big sea of DNA sequences. KGGSeq has paid attention to downstream analysis of genetic mapping. The framework was implemented to filter and prioritize genetic variants from whole exome sequencing data.

Proper citation: KGGSeq (RRID:SCR_005311) Copy   

•   Source: SciCrunch Registry

http://soap.genomics.org.cn/soapindel.html

Software focusing on calling indels from the next-generation paired-end sequencing data.

Proper citation: SOAPindel (RRID:SCR_005272) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/PING.html

Software program for probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach.

Proper citation: PING (RRID:SCR_005394) Copy   

•   Source: SciCrunch Registry

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

Software package to comprehensively evaluate different aspects of RNA-seq experiments, such as sequence quality, GC bias, polymerase chain reaction bias, nucleotide composition bias, sequencing depth, strand specificity, coverage uniformity and read distribution over the genome structure. RSeQC takes both SAM and BAM files as input, which can be produced by most RNA-seq mapping tools as well as BED files, which are widely used for gene models.

Proper citation: RSeQC (RRID:SCR_005275) Copy   

•   Source: SciCrunch Registry

http://bioapps.sabanciuniv.edu/mugex/v02/

Service that automatically extracts mutation-gene pairs from MEDLINE abstracts for a given disease.

Proper citation: MuGeX (RRID:SCR_005306) Copy   

•   Source: SciCrunch Registry