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http://sourceforge.net/projects/pyqpcr/

A GUI application written in python that deals with quantitative PCR (QPCR) raw data. Using quantification cycle values extracted from QPCR instruments, it uses a proven and universally applicable model to give finalized quantification resu

Proper citation: pyQPCR (RRID:SCR_000471) Copy   

•   Source: SciCrunch Registry

http://drfast.sourceforge.net/

A software which maps di-base reads (SOLiD color space reads) to reference genome assemblies in a fast and memory-efficient manner.

Proper citation: drFAST (RRID:SCR_000586) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/gmcloser/

Software that fills and closes the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads. Unlike other gap-closing tools that use only NGS reads, GMcloser uses preassembled contig sets or long read sets as the sequences to close gaps and uses paired-end (PE) reads and a likelihood-based algorithm to improve the accuracy and efficiency of gap closure. The efficiency of gap closure can be increased by successive treatments with different contig sets.

Proper citation: GMcloser (RRID:SCR_000646) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/detecttd/

Software tool to detect tandem duplications in sequencing reads. It is written in Python and requires NCBI Blast standalone.

Proper citation: detecttd (RRID:SCR_000681) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/fastuniq/

A software tool for removal of de novo duplicates in paired short DNA sequences.

Proper citation: FastUniq (RRID:SCR_000682) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/triagetools/

A collection of tools for partitioning raw data (fastq reads) from high-throughput sequencing projects. The tools are designed for basic data management as well for prioritizing analysis of certain subsets.

Proper citation: TriageTools (RRID:SCR_000675) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ngs-toolbox/

A collection of simple Perl scripts adressed to scientists doing research that bases on high throughput genomic/transcriptomic data. It does not require any bioinformatic expertise. The scripts perform fundamental processing steps like sorting sequences by TAGs, FASTQ to FASTA conversion, filtering and counting of redundant sequences, individually adjustable FASTQ quality filtering or basic analyses like base count and analysis of sequence length distribution.

Proper citation: NGS tools for the novice (RRID:SCR_000664) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/operasf/

A sequence assembly software program that uses information from paired-end reads to optimally order and orient contigs assembled from shotgun-sequencing reads.

Proper citation: Opera (RRID:SCR_000665) Copy   

•   Source: SciCrunch Registry

http://biolemmatizer.sourceforge.net/

A domain-specific lemmatization software tool for the morphological analysis of biomedical literature.

Proper citation: BioLemmatizer (RRID:SCR_000117) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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/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://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

http://sourceforge.net/projects/viralfusionseq/

A versatile high-throughput sequencing (HTS) tool for discovering viral integration events and reconstruct fusion transcripts at single-base resolution. It combines soft-clipping information, read-pair analysis, and targeted de novo assembly to discover and annotate viral-human fusion events. A simple yet effective empirical statistical model is used to evaluate the quality of fusion breakpoints. Minimal user defined parameters are required.

Proper citation: VFS (RRID:SCR_005138) Copy   

•   Source: SciCrunch Registry