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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
http://sourceforge.net/projects/hlaseq/
An open-source software tool for accurate genotyping the human HLA genes from Illumina GA high-throughput sequencing data.
Proper citation: HLASeq (RRID:SCR_004185) Copy
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
http://www.sanger.ac.uk/science/tools/olorin
An interactive filtering tool for next generation sequencing data coming from the study of large complex disease pedigrees. It integrates gene flow output from Merlin and next generation sequencing data. Users can interactively filter and prioritize variants based on haplotype sharing across different sets of selected individuals and allele frequency in reference datasets. (entry from Genetic Analysis Software)
Proper citation: OLORIN (RRID:SCR_002015) Copy
http://unoseq.sourceforge.net/
A Java library to analyze next generation sequencing data and especially perform expression profiling in organisms where no well-annotated reference genome exists.
Proper citation: UnoSeq (RRID:SCR_005116) Copy
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
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
http://sourceforge.net/projects/quasr/
A lightweight software pipeline written to process and analyse next-generation sequencing (NGS) data from Illumina, 454, and Ion Torrent platforms. Although originally written for viral data, it is generic enough to work on any NGS dataset. Functions include: duplicate removal, demultiplexing, primer-removal, quality-assurance (QA) graphing, quality control (QC), consensus-generation, minority-variant determination, minority-variant graphing.
Proper citation: QUASR (RRID:SCR_006820) Copy
http://sourceforge.net/projects/bigpre/
A quality assessment software package for next-genomics sequencing data.
Proper citation: BIGpre (RRID:SCR_006781) Copy
http://sourceforge.net/projects/taxoassignement/
Software tool for the taxonomic assignment of Next Generation Sequencing reads using multiple reference taxonomy.
Proper citation: TaxoAssignement (RRID:SCR_006814) Copy
http://sourceforge.net/projects/insertionmapper/
A pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data. It consists of four independently working modules: Data Preprocessing, Database Modeling, Dimension Deconvolution and Element Mapping. This pipeline tool is applicable to scenarios requiring analysis of the tremendous output of short reads produced in NGS sequencing experiments of targeted genome sequences.
Proper citation: InsertionMapper (RRID:SCR_004163) Copy
Ratings or validation data are available for this resource
http://broadinstitute.github.io/picard/
Java toolset for working with next generation sequencing data in the BAM format.
Proper citation: Picard (RRID:SCR_006525) Copy
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