Tools   Select Another Resource Report Type

http://srf.sourceforge.net/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://ribopicker.sourceforge.net/

Software to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets.

Proper citation: riboPicker (RRID:SCR_000360) Copy   

•   Source: SciCrunch Registry

http://parsecnv.sourceforge.net/

Software that takes CNV calls as input and creates SNP based statistics for CNV occurrence in cases and controls then calls CNVRs based on neighboring SNPs of similar significance.

Proper citation: ParseCNV (RRID:SCR_000355) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/kinannote/

Software that identifies and classifies protein kinases in a user-provided fasta file using an HMM derived from serine / threonine protein kinases, a position specific scoring matrix derived from the HMM, and comparison with a local version of the curated kinase database from kinase.com.

Proper citation: Kinannote (RRID:SCR_000352) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/jnomics/

A collection of cloud-scale DNA sequence analysis tools.

Proper citation: Jnomics (RRID:SCR_000348) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/fqzcomp/

A basic fastq compressor, designed primarily for high performance.

Proper citation: fqzcomp (RRID:SCR_000299) Copy   

•   Source: SciCrunch Registry

http://compbio.cs.sfu.ca/software-variation-hunter

A software tool for discovery of structural variation in one or more individuals simultaneously using high throughput technologies.

Proper citation: VariationHunter (RRID:SCR_004865) Copy   

•   Source: SciCrunch Registry

http://pythia.sourceforge.net/

Pythia is an open source thermodynamically oriented primer design python module. Pythia can be used in two ways. 1. Executable binaries only: under windows with cygwin and python 2.5 (built with mingw, that comes with the cygwin release). These executables allow the user to index DNA files for primer specificity search, design one primer pair per region, and tile regions with PCR amplicons. 2. A python module: under windows with cygwin, python2.5, numpy, swig, and mingw, or under linux with python2.4 or later, numpy, and swig (everything but numpy should be pre-installed on a normal linux system). The module gets you everything that the binaries get you, in a more pythonic framework. This package also includes modules for computing DNA binding and folding energies using the partition function approach with publicly available thermodynamic data. Usage documentation is in the downloads.

Proper citation: Pythia (RRID:SCR_004952) 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://sourceforge.net/apps/mediawiki/amos/index.php?title=Bambus2

Software for scaffolding to address some of the challenges encountered when analyzing metagenomes. Scaffolding represents the task of ordering and orienting contigs by incorporating additional information about their relative placement along the genome. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with great flexibility in choosing the scaffolding parameters. In particular, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the output of MUMmer), physical mapping data, or information about gene synteny.

Proper citation: Bambus (RRID:SCR_005068) Copy   

•   Source: SciCrunch Registry

http://www.comp.hkbu.edu.hk/~chxw/software/G-BLASTN.html

A GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST. It can produce exactly the same results as NCBI-BLAST, and it also has very similar user commands. It also supports a pipeline mode, which can fully utilize the GPU and CPU resources when handling a batch of medium to large sized queries.

Proper citation: G-BLASTN (RRID:SCR_005062) Copy   

•   Source: SciCrunch Registry