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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
http://biolemmatizer.sourceforge.net/
A domain-specific lemmatization software tool for the morphological analysis of biomedical literature.
Proper citation: BioLemmatizer (RRID:SCR_000117) Copy
http://soap.genomics.org.cn/soapfuse.html
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on August 23,2022. An open source tool developed for genome-wide detection of fusion transcripts from human being paired-end RNA-Seq data. This tool is a part of a larger set of tools to efficiently align oligonucleotides onto reference sequences .
Proper citation: SOAPfuse (RRID:SCR_000078) Copy
A generic format for DNA sequence data. The primary motivation for creating SRF has been to enable a single format capable of storing data generated by any DNA sequencing technology.
Proper citation: Sequence Read Format (RRID:SCR_000132) Copy
http://sourceforge.net/projects/exomesuite/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software application designed to analyze variant call files from next generation sequencing data to identify variants causing disease.
Proper citation: exomeSuite (RRID:SCR_000129) Copy
https://github.com/lskatz/cg-pipeline
A software tool for assembling genome sequence data and running feature prediction and annotation tools on the assembly.
Proper citation: CG-Pipeline (RRID:SCR_000047) Copy
http://sourceforge.net/projects/rnaseqvariantbl/
Open source software tool that simulates experimental RNA-seq and DNA whole exome sequences derived from reference genome, aligns these sequences by custom parameters, detects variants and outputs blacklist of positions and alleles caused by mismapping. Used to characterize mappability of RNA-Seq reads and create blacklist of genomic positions of mismapped reads. This blacklist is used to filter potential false positives from variant or RNA editing calls.
Proper citation: BlackOPs (RRID:SCR_000032) Copy
http://sourceforge.net/projects/batman-seq/
A fast BWT-based short reads mapping tools which uses additional statistical method to model error profile of the sequencing experiment.
Proper citation: Batman-Seq (RRID:SCR_000048) Copy
http://sourceforge.net/projects/ms-spectre/
Software that provides (Quantitiave) analysis of multiple ls-ms(ms) runs, using mzXML import of raw data coming from spectrometers.
Proper citation: MS-Spectre (RRID:SCR_000266) Copy
http://sourceforge.net/projects/blastplot/
A PERL module that can quickly plot the BLAST results from short sequences (primers, probes, reads) against reference targets. This software generates PNG graphs for all of the reference sequences associated with a BLAST result set.
Proper citation: BLASTPLOT (RRID:SCR_000162) Copy
http://sourceforge.net/projects/gemsim/
A software package for generating realistic simulated next-generation genome sequencing reads with quality score values. The software is written in Python with a command-line user interface.
Proper citation: GemSIM (RRID:SCR_000167) Copy
http://sourceforge.net/projects/gmato/files/?source=navbar
A software tool used for simple sequence repeats (SSR) or microsatellite characterization. It also facilitates SSR marker design on a genomic scale, microsatellite mining at any length, and comprehensive statistical analysis for DNA sequences in any genome at any size. Analysis parameters are customizable.
Proper citation: GMATo (RRID:SCR_000165) Copy
http://proteinprophet.sourceforge.net/
Software that automatically validates protein identifications made on the basis of peptides assigned to MS/MS spectra by database search programs such as SEQUEST.
Proper citation: ProteinProphet (RRID:SCR_000286) Copy
http://sourceforge.net/projects/taipan/
A fast hybrid short-read assembly tool.
Proper citation: Taipan (RRID:SCR_007330) Copy
http://genotan.sourceforge.net/
A free software tool to identify length variation of microsatellites from short sequence reads.
Proper citation: GenoTan (RRID:SCR_007935) Copy
A cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data.
Proper citation: BRIG (RRID:SCR_007802) Copy
http://seqpig.sourceforge.net/
A software library for Apache Pig for the distributed analysis of large sequencing datasets on Hadoop clusters.
Proper citation: SeqPig (RRID:SCR_008548) Copy
http://splitread.sourceforge.net/
Software for detecting INDELs (small insertions and deletion with size less than 50bp) as well as large deletions that are within the coding regions from the exome sequencing data. It also can be applied to the whole genome sequencing data.
Proper citation: SPLITREAD (RRID:SCR_005264) Copy
A set of programs that map and assemble fixed-length Solexa/SOLiD reads in a fast and accurate way.
Proper citation: Maq (RRID:SCR_005485) Copy
http://chipexo.sourceforge.net/
A bioinformatics tool dedicated to analyze ChIP-exo data: 1) Sequencing depth normalization and nucleotide composition bias correction. 2) Signal consolidation and noise reduction. 3) Single base resolution border detection. 4) Border matching.
Proper citation: MACE (RRID:SCR_005520) Copy
http://sourceforge.net/p/treq/home/Home/
A software read mapper for high-throughput DNA sequencing reads, in particular one to several hundred nucleotides in length, and for large edit distance between sequencing read and match in the reference genome. It can cope particularly well with indels for single-best hit recall of 200nt reads simulated from the human reference genome. TreQ performs best at a running time comparable to BWA at large edit distance settings.
Proper citation: TreQ (RRID:SCR_005505) Copy
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