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https://github.com/friend1ws/EBCall

A software package for somatic mutation detection (including InDels). EBCall uses not only paired tumor/normal sequence data of a target sample, but also multiple non-paired normal reference samples for evaluating distribution of sequencing errors, which leads to an accurate mutaiton detection even in case of low sequencing depths and low allele frequencies.

Proper citation: EBCall (RRID:SCR_006791) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/bamstats/

A GUI desktop tool for calculating and displaying metrics to assess the success of Next Generation Sequencing mapping tools. BAMstats is written in Java and based around the Picard API.

Proper citation: BAMStats (RRID:SCR_006973) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/2.9/bioc/html/RamiGO.html

Software package with an R interface sending requests to AmiGO visualize, retrieving DAG GO trees, parsing GraphViz DOT format files and exporting GML files for Cytoscape. Also uses RCytoscape to interactively display AmiGO trees in Cytoscape.

Proper citation: RamiGO (RRID:SCR_006922) Copy   

•   Source: SciCrunch Registry

http://www.seqan.de/projects/razers/

A read mapping software program with adjustable sensitivity based on counting q-grams. RazerS 3 supports shared-memory parallelism, an additional seed-based filter with adjustable sensitivity, a much faster, banded version of the Myers? bit-vector algorithm for verification, memory saving measures and support for the SAM output format. This leads to a much improved performance for mapping reads, in particular long reads with many errors.

Proper citation: RazerS (RRID:SCR_006889) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/artfastqgen/

Software to evaluate and improve the accuracy of sequencing error under different experimental conditions. It can identify which components of a system may be suboptimal and which regions of the genome may be problematic.

Proper citation: ArtificialFastqGenerator (RRID:SCR_006880) 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://code.google.com/p/crop-tingchenlab/

A clustering tool designed mainly for Metagenomics studies, which clusters 16S rRNA sequences into Operational Taxonomic Units (OTU). By using a Gaussian Mixture model, CROP can automatically determine the best clustering result for 16S rRNA sequences at different phylogenetic levels without setting a hard cutoff threshold as hierarchical clustering does. Yet, at the same time, it is able to manage large datasets and to overcome sequencing errors.

Proper citation: CROP (RRID:SCR_006916) Copy   

•   Source: SciCrunch Registry

http://math.mcb.berkeley.edu/~meromit/MetMap/

A computational pipeline for the analysis of MethylSeq experiments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MetMap (RRID:SCR_006954) Copy   

•   Source: SciCrunch Registry

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

A cloud computing tool for calculating differential gene expression in large RNA-seq datasets. It uses Bowtie for short read alignment and R/Bioconductor for interval calculations, normalization, and statistical testing. These tools are combined in an automatic, parallel pipeline that runs in the cloud (Elastic MapReduce in this case) on a local Hadoop cluster, or on a single computer, exploiting multiple computers and CPUs wherever possible.

Proper citation: Myrna (RRID:SCR_006951) Copy   

•   Source: SciCrunch Registry

http://genome.ufl.edu/rivalab/pasta/

A complete pipeline for the analysis of alternative splicing using RNA-Sequencing data.

Proper citation: PASTA (RRID:SCR_008770) Copy   

•   Source: SciCrunch Registry

http://www.raetschlab.org/suppl/qpalma

An alignment tool targeted to align spliced reads produced by Next Generation sequencing platforms such as Illumina Solexa or 454.

Proper citation: QPALMA (RRID:SCR_008791) Copy   

•   Source: SciCrunch Registry

http://r-forge.r-project.org/projects/sequgio/

An algorithm to estimate isoforms expression from RNA-seq data based on a model that doesn''t assume uniform distribution of count within transcripts.

Proper citation: Sequgio (RRID:SCR_008867) Copy   

•   Source: SciCrunch Registry

http://lrcv-crp-sante.s3-website-us-east-1.amazonaws.com/

A gene set analysis algorithm for biomarker identification in the cloud.

Proper citation: YunBe (RRID:SCR_008740) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.fccc.edu/software/OpenSource/FGDP/FGDP.shtml

A Java-based, Microarray or Genechip data analysis system.

Proper citation: FGDP (RRID:SCR_008910) Copy   

•   Source: SciCrunch Registry

http://www.biomedcentral.com/1471-2105/14/357/abstract

Sample size calculation based on exact test for assessing differential expression analysis in RNA-seq data. R code is available from the corresponding author.

Proper citation: A sample size calculation method (RRID:SCR_009469) Copy   

•   Source: SciCrunch Registry

http://www.cibiv.at/~niko/ngc/

A compressor for aligned HTS sequencing data that enables the complete lossless and lossy compression of mapped alignment data stored in SAM/BAM files.

Proper citation: NGC (RRID:SCR_009342) Copy   

•   Source: SciCrunch Registry

http://geckoe.sourceforge.net/

A complete, high-capacity centralized gene expression analysis system, developed in response to the needs of a distributed user community.

Proper citation: Gecko (RRID:SCR_009001) Copy   

•   Source: SciCrunch Registry

http://homes.cs.washington.edu/~dcjones/quip/

Compresses next-generation sequencing data in the FASTQ and SAM/BAM formats with extreme prejudice.

Proper citation: Quip (RRID:SCR_009362) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.ua.pt/software/mfcompress/

A compression tool for FASTA and multi-FASTA files.

Proper citation: MFCompress (RRID:SCR_009301) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.research.nicta.com.au/software/rlz/

Optimized relative Lempel-Ziv compression of genomes.

Proper citation: RLZ (RRID:SCR_009420) Copy   

•   Source: SciCrunch Registry