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http://sourceforge.net/projects/amos/

A collection of tools and class interfaces for the assembly of DNA reads.

Proper citation: AMOS (RRID:SCR_013067) Copy   

•   Source: SciCrunch Registry

http://aluru-sun.ece.iastate.edu/doku.php?id=reptile

A software developed in C++ for correcting sequencing errors in short reads from next-gen sequencing platforms.

Proper citation: Reptile (RRID:SCR_013075) Copy   

•   Source: SciCrunch Registry

http://microbiomeutil.sourceforge.net/#A_CS

A chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500 bp).

Proper citation: ChimeraSlayer (RRID:SCR_013283) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/telescoper/

An algorithm that iteratively extends long paths through a series of read-overlap graphs and evaluates them based on a statistical framework.

Proper citation: Telescoper (RRID:SCR_013206) Copy   

•   Source: SciCrunch Registry

http://alumni.cs.ucr.edu/~liw/isolasso.html

An algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads.

Proper citation: IsoLasso (RRID:SCR_013176) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/heuraa/

Software for accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing.

Proper citation: HeurAA (RRID:SCR_013212) Copy   

•   Source: SciCrunch Registry

http://bioinfo.ctb.pku.edu.cn/MAP/

This resource is out of service. Documented on February 23,2021. Software for de novo metagenomic assembly program for shotgun DNA reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MAP (RRID:SCR_013216) Copy   

•   Source: SciCrunch Registry

http://bowtie-bio.sourceforge.net/crossbow/index.shtml

A scalable software pipeline for whole genome resequencing analysis.

Proper citation: Crossbow (RRID:SCR_013306) Copy   

•   Source: SciCrunch Registry

http://tomcatbackup.esat.kuleuven.be/inclusive/

A suit of algorithms and tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements.

Proper citation: INCLUSive (RRID:SCR_013488) Copy   

•   Source: SciCrunch Registry

http://hannonlab.cshl.edu/Alta-Cyclic/main.html

An Illumina Genome-Analyzer (Solexa) base caller.

Proper citation: Alta-Cyclic (RRID:SCR_013373) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software providng a method based on Bayes? theorem (the reverse probability model) to call consensus genotype by carefully considering the data quality, alignment, and recurring experimental errors., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SOAPsnp (RRID:SCR_010602) Copy   

•   Source: SciCrunch Registry

http://noble.gs.washington.edu/proj/crux/

A software toolkit for tandem mass spectrometry analysis, with a focus on peptide identification. Crux analyzes shotgun proteomics tandem mass spectra, associating peptides with observed spectra. This software toolkit for tandem mass spectrometry analysis, with a focus on peptide identification is provided as a single executable. Crux is implemented in C and is distributed with source code freely to noncommercial users. Mass spectrometry, the core technology in the field of proteomics, promises to enable scientists to identify and quantify the entire complement of proteins in a complex biological sample. Currently, the primary bottleneck in this type of experiment is computational. Existing algorithms for interpreting mass spectra are slow and fail to identify a large proportion of the given spectra. We describe a database search program called Crux that reimplements and extends the widely used database search program Sequest. For speed, Crux uses a peptide indexing scheme to rapidly retrieve candidate peptides for a given spectrum. For each peptide in the target database, Crux generates shuffled decoy peptides on the fly, providing a good null model and, hence, accurate false discovery rate estimates. Crux also implements two recently described postprocessing methods: a p value calculation based upon fitting a Weibull distribution to the observed scores, and a semisupervised method that learns to discriminate between target and decoy matches. Both methods significantly improve the overall rate of peptide identification.

Proper citation: Crux tandem mass spectrometry analysis software (RRID:SCR_010648) Copy   

•   Source: SciCrunch Registry

http://snpinfo.niehs.nih.gov/

SNPinfo Web Server is a set of freely available web-based SNP selection tools where investigators can specify genes or linkage regions and select SNPs based on GWAS results, linkage disequilibrium (LD), and predicted functional characteristics of both coding and non-coding SNPs. The algorithm uses GWAS SNP P-value data and finds all SNPs in high LD with GWAS SNPs, so that selection is from a much larger set of SNPs than the GWAS itself. The program can also identify and choose tag SNPs for SNPs not in high LD with any GWAS SNP. We incorporate functional predictions of protein structure, gene regulation, splicing and miRNA binding, and consider whether the alternative alleles of a SNP are likely to have differential effects on function. Users can assign weights for different functional categories of SNPs to further tailor SNP selection. The program accounts for LD structure of different populations so that a GWAS study from one ethnic group can be used to choose SNPs for one or more other ethnic groups. SNP Selection and Functional Information *Candidate Gene SNP Selection (GenePipe):SNP selection for candidate genes based on Genome Wide Association Study (GWAS) results, functional SNP prediction and Linkage Disequilibrium (LD) information. *GWAS Functional SNP Selection (GenomePipe):Functional SNP selection from SNPs that are in high LD with GWAS SNPs *GWAS SNP Selection in Linkage Loci (LinkagePipe):GWAS SNP selection in candidate genomic regions (such as linkage loci) *LD TAG SNP Selection (TagSNP):LD tag SNP selection and visualization for single or multiple populations. Finalization of SNP list from various queries. *SNP Function Prediction (FuncPred): Querying SNP function predictions and ethnic-specific allele frequencies. *SNP Information in DNA Sequence (SNPseq):Visualization of SNP related information in the context of DNA sequence. Preparing DNA Sequence for PCR Primer Design considering SNP information. Detailed information of CpG region.

Proper citation: SNPinfo Web Server (RRID:SCR_010589) Copy   

•   Source: SciCrunch Registry

http://cseweb.ucsd.edu/~ppevzner/software.html#EULER-short

Assembly package that contains a suite of software programs for correcting errors in short reads and assembling them. The assembler may take as input classical Sanger reads, 454 sequences, and Illumina reads.

Proper citation: EULER-SR (RRID:SCR_010485) Copy   

•   Source: SciCrunch Registry

http://home.gwu.edu/~wpeng/Software.htm

A clustering software package for identification of enriched domains from histone modification ChIP-Seq data.

Proper citation: SICER (RRID:SCR_010843) Copy   

•   Source: SciCrunch Registry

http://www.netlab.uky.edu/p/bioinfo/MapSplice

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. Accurate mapping of RNA-seq reads for splice junction discovery.

Proper citation: MapSplice (RRID:SCR_010844) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/p/mira-assembler/wiki/Home/

Sequence assembler and mapper for whole genome shotgun and EST/RNASeq sequencing data.

Proper citation: MIRA (RRID:SCR_010731) Copy   

•   Source: SciCrunch Registry

http://mocklerlab.org/tools/2

A quality-value guided de novo short read assembler.

Proper citation: QSRA (RRID:SCR_010733) Copy   

•   Source: SciCrunch Registry

http://genetics.cs.ucla.edu/harsh/

Software that provides a method to infer the haplotype using haplotype reference panel and high throughput sequencing data.

Proper citation: HARSH (RRID:SCR_010792) Copy   

•   Source: SciCrunch Registry

http://www.bioinf.jku.at/research/short-IBD/

Software that identifies short identity by descent (IBD) segments that are tagged by rare variants in large sequencing data.

Proper citation: HapFABIA (RRID:SCR_010793) Copy   

•   Source: SciCrunch Registry