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http://sourceforge.net/projects/variantmaster/

Software program that extracts causative variants in familial and sporadic genetic diseases. The algorithm takes into account predicted variants (SNPs and indels) in affected individuals or tumor samples and utilizes the row (BAM) data to robustly estimate the conditional probability of segregation in a family, as well as the probability of it being de novo or somatic. In familial cases, various modes of inheritance are considered: X-linked, autosomal dominant, and recessive (homozygosity or compound heterozygosity). Moreover, it integrates phenotypes and genotypes, and employs Annovar to produce additional information as allelic frequencies in general population and damaging scores.

Proper citation: VariantMaster (RRID:SCR_000569) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/denovogear/

A software for detecting de novo mutations using sequencing data. It utilizes likelihood-based error modeling to reduce the false positive rate of mutative discovery in exome analysis. It also uses fragment information to identify the parental origin of germ-line mutations.

Proper citation: DeNovoGear (RRID:SCR_000670) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/srma/

A post-alignment micro re-aligner for next-generation high throughput sequencing data.

Proper citation: SRMA (RRID:SCR_000669) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/finesplice/

A software pipeline based on TopHat2 combined with a splice junction detection algorithm.

Proper citation: FineSplice (RRID:SCR_000691) Copy   

•   Source: SciCrunch Registry
  

http://crossmap.sourceforge.net/

A software program for convenient conversion of genome coordinates (or annotation files) between different assemblies. It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF. It is designed to liftover genome coordinates between assemblies. It?s not a program for aligning sequences to reference genome. CrossMap is not recommend for converting genome coordinates between species.

Proper citation: CrossMap (RRID:SCR_001173) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/particlecall/

A base-calling algorithm for Illumina DNA sequencing.

Proper citation: ParticleCall (RRID:SCR_001103) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/sparseassembler/

Software for memory-efficient genome assembly. It utilizes sparse k-mer.

Proper citation: SparseAssembler (RRID:SCR_001100) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/cuda-ec/

A fast parallel error correction tool for short reads.

Proper citation: CUDA-EC (RRID:SCR_001090) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/qips/

A software package for analyzing ChIP-seq (Chromatin ImmunoPrecipitation on sequencing) data that finds enriched regions of arbitrary lengths and is therefore especially suited for analyzing ChIP-seq of histone marks or polymerase.

Proper citation: qips (RRID:SCR_001092) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/apps/mediawiki/breakway/index.php

A suite of software programs that take aligned genomic data and report structural variation breakpoints. Features include: * Takes in BAM formatted input, the current standard for genomic alignments. * Compatible with standard output from major alignment algorithms such as BFAST, BWA, MAQ, et cetera. * Capable of analyzing data from any major platform--Solexa, SOLiD, 454, et cetera. * Empirically identifies structural variation breakpoints. * Highly specific analysis generates very few false positives. * Includes a suite of downstream tools for annotating identified breakpoints and reducing false positives.

Proper citation: Breakway (RRID:SCR_001180) Copy   

•   Source: SciCrunch Registry
  

https://gitlab.sib.swiss/EPD/chipseq

Set of software modules for performing common ChIP-seq data analysis tasks across the whole genome, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. The tools are designed to be simple, fast and highly modular. Each program carries out a well-defined data processing procedure that can potentially fit into a pipeline framework. ChIP-Seq is also freely available on a Web interface.

Proper citation: ChIP-seq (RRID:SCR_001237) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/ngsrich/

Software for target enrichment performance for next-generation sequencing.

Proper citation: NGSrich (RRID:SCR_001333) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/cohcap/

An algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). It provides QC metrics, differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, and visualization of methylation values.

Proper citation: COHCAP (RRID:SCR_006499) Copy   

•   Source: SciCrunch Registry
  

http://garm-meta-assem.sourceforge.net/

A new software pipeline to merge and reconcile assemblies from different algorithms or sequencing technologies.

Proper citation: GARM (RRID:SCR_006731) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/blox/

A quantitative medical imaging and visualization program for use on brain MR, DTI, and MRS data. Programming Language: Java, JavaScript, Scheme

Proper citation: Blox (RRID:SCR_006667) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/powermap/

Software tool specifically designed for neuroimaging data that implements theoretical power calculation algorithms based on non-central random field theory. It can also calculate power for statistical analyses with FDR (false discovery rate) corrections. This GUI (graphical user interface)-based tool enables neuroimaging researchers without advanced knowledge in imaging statistics to calculate power and sample size in the form of 3D images. This tool is currently under limited release for beta testing. At this time, only users that have been directed to this site by the PowerMap developers will receive support.

Proper citation: PowerMap (RRID:SCR_006721) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/samscope/

A lightweight SAM/BAM file viewer that makes visually exploring next generation sequencing data intuitive and maybe even fun! Quickly and easily generate aggregate statistics from SAM/BAM files like coverage, polarity, and minor allele frequencies, then scroll and explore freely with a simple mouse based interface. Multiple windows can be synchronized for careful comparison across multiple experiments.

Proper citation: Samscope (RRID:SCR_006715) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/dmeas/

A user-friendly DNA methylation analysis tool for DNA methylation pattern extraction, DNA methylation level estimation, DNA methylation entropy analysis and multi-sample comparison. It was developed in order to assess the DNA methylation variations for a given genomic locus or genome-wide methylation data.

Proper citation: DMEAS (RRID:SCR_006679) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/hiahia/

A sequence alignment tool to align both short and long reads to a reference genome. HIA has two indexes, a hash table index and a suffix array index. The hash table is capable of the direct lookup of a q-gram and the suffix array is very fast in the lookup of a variable length q-gram. Our experiments show that the hybrid of hash table and suffix array is useful at the perspective of speed to map NGS sequencing reads to a reference genome sequence.

Proper citation: HIA (RRID:SCR_006865) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/fitgcp/

Software providing a framework for fitting mixtures of probability distributions to genome coverage profiles.

Proper citation: fitGCP (RRID:SCR_006741) Copy   

•   Source: SciCrunch Registry