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http://sourceforge.net/projects/vcake/

A genetic sequence assembler capable of assembling millions of small nucleotide reads even in the presence of sequencing error.

Proper citation: VCAKE (RRID:SCR_013060) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/conifer/

Uses exome sequencing data to find copy number variants (CNVs) and genotype the copy-number of duplicated genes.

Proper citation: CoNIFER (RRID:SCR_013213) Copy   

•   Source: SciCrunch Registry
  

http://rdxplorer.sourceforge.net/

A computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage.

Proper citation: RDXplorer (RRID:SCR_013290) Copy   

•   Source: SciCrunch Registry
  

http://nipy.org

Community site to make brain imaging research easier that aims to build software that is clearly written, clearly explained, a good fit for the underlying ideas, and a natural home for collaboration.

Proper citation: Neuroimaging in Python (RRID:SCR_013141) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/pia2/

A prefix indexing and alignment software for next-generation sequencing (NGS) for whole human genome.

Proper citation: PIA (RRID:SCR_013267) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/mirseq/files/

An R/Bioconductor based workflow for novel miRNA prediction from deep sequencing data.

Proper citation: miRSeqNovel (RRID:SCR_013257) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/dynamicprog/

A model-based statistical methods for base calling in Illumina''s next-generation sequencing platforms.

Proper citation: DynamicProg (RRID:SCR_013217) Copy   

•   Source: SciCrunch Registry
  

http://beads.sourceforge.net/

Software for a normalization scheme that corrects nucleotide composition bias, mappability variations and differential local DNA structural effects in deep sequencing data.

Proper citation: BEADS (RRID:SCR_013229) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/congrpe/

A de novo assembly algorithm for Next-Generation Sequencing technology.

Proper citation: CongrPE (RRID:SCR_013190) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/callsim/

A software application that provides evidence for the validity of base calls believed to be sequencing errors and it is applicable to Ion Torrent and 454 data.

Proper citation: CallSim (RRID:SCR_013192) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/sapas/

A RNA-seq method for polyA research.

Proper citation: SAPAS (RRID:SCR_013195) Copy   

•   Source: SciCrunch Registry
  

http://arrayoligosel.sourceforge.net/

Software program to systematically design gene specific long oligonucleotide probes for entire genomes, for the purpose of developing whole genome microarrays. For each open reading frame, the program optimizes the oligo selection based upon several parameters, including uniqueness in the genome, sequence complexity, lack of self-binding, GC content and proximity to the 3''end of the gene.

Proper citation: ArrayOligoSelector (RRID:SCR_013494) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/splicegrapher/

Software that predicts alternative splicing patterns and produces splice graphs that capture in a single structure the ways a gene''s exons may be assembled. It enhances gene models using evidence from next-generation sequencing and EST alignments.

Proper citation: SpliceGrapher (RRID:SCR_006657) Copy   

•   Source: SciCrunch Registry
  

http://seqbarracuda.sourceforge.net/

A sequence mapping software that utilizes the massive parallelism of graphics processing units to accelerate the inexact alignment of short sequence reads to a particular location on a reference genome. It can align a paired-end library containing 14 million pairs of 76bp reads to the Human genome in about 27 minutes (from fastq files to SAM alignment) using a ��380 NVIDIA Geforce GTX 680*. The alignment throughput can be boosted further by using multiple GPUs (up to 8) at the same time. Being based on BWA (http://bio-bwa.sf.net) from the Sanger Institute, BarraCUDA delivers a high level of alignment fidelity and is comparable to other mainstream alignment programs. It can perform gapped alignment with gap extensions, in order to minimise the number of false variant calls in re-sequencing studies.

Proper citation: BarraCUDA (RRID:SCR_006881) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/polgui/

An interface between MATLAB and the Polhemus Fastrak digitizer used to digitize fiducial locations and scalp EEG electrode locations. There are 5 versions all of which work under MATLAB R14 (on both linux and windows platforms), # polgui_ver1_r14 : works with 1 receiver (stylus pen) # polgui_ver2_r14 : works with 2 receivers (including the pen) # polgui_ver3_r14 : works with 3 receivers(including the pen) # polgui_ver4_r14 : works with 4 receivers (including the pen) # polgui_ver5_r14 : Generic version which works with 1/2/3/4 receivers (WARNING: Ver 5 might be buggy; not fully tested) Requirements: MATLAB R14 (Linux/Windows)

Proper citation: POLGUI - Matlab Polhemus Interface (RRID:SCR_006752) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/bmdexpress/

Bioinformatics tool used to analyze microarray dose-response data. The analysis provides benchmark dose estimates at which different cellular processes are altered in toxicogenomic experiments.

Proper citation: BMDExpress (RRID:SCR_006823) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/mubiomics/

A set of scripts (mostly python) for processing reads generated by the Roche 454 or Illumina next-gen sequencing platforms. Included are quality control, read demultiplexing and microbiome characterisation scripts for use with usearch, pplacer and RDP classifier.

Proper citation: mubiomics (RRID:SCR_006785) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/qudaich/

A software package for local sequence alignment for next-generation sequencing (NGS) data. It generates the pairwise local alignments between a query dataset against a database. The main design purpose of qudaich is to focus on datasets from next generation sequencing. These the datasets generally have hundreds of thousand sequences or more, and so, the input database should contain large number of sequences. Qudaich is flexible and its algorithmic structure imposes no restriction on the absolute limit of the acceptable read length, but the current version of qudaich allow read length <2000 bp. Qudaich can be used to align DNA, translated DNA and protein sequences.

Proper citation: Qudaich (RRID:SCR_006775) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/aeo/

AEO represents the Adverse Event Ontology, a community-driven ontology developed to standardize and integrate data on biomedical adverse events (e.g., vaccine adverse events) and support computer-assisted reasoning. The AEO also can be found in BioPortal, http://bioportal.bioontology.org/ontologies/45534?p=terms

Proper citation: Adverse Event Ontology (RRID:SCR_006807) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/gbsbarcode/

PERL script used to split barcode of Illumina sequencing data created by GBS protocol (www.maizegenetics.net). The barcode has variable size. Paired-end reads are supported.

Proper citation: GBS barcode splitter (RRID:SCR_006799) Copy   

•   Source: SciCrunch Registry