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http://sourceforge.net/projects/palfinder/
A perl script that finds microsatellite repeat elements directly from raw 454 or Illumina paired-end sequencing reads.
Proper citation: palfinder (RRID:SCR_013174) Copy
http://sourceforge.net/projects/samcomp/
A simple arithmetic coding based compressor for the SAM and BAM (DNA sequence alignment) file format.
Proper citation: sam comp (RRID:SCR_013179) Copy
http://sourceforge.net/projects/heuraa/
Software for accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing.
Proper citation: HeurAA (RRID:SCR_013212) Copy
http://sourceforge.net/projects/bisreadmapper/
Fast and lightweight package for mapping bisulfite converted DNA sequencing reads from the Illumina platform.
Proper citation: bisReadMapper (RRID:SCR_013171) Copy
http://sourceforge.net/projects/celeragb/
Software developed at Celera Genomics as part of Celera''s sequencing and annotation of the human genome, and released as open source in 2006.
Proper citation: Celera Genome Browser (RRID:SCR_013093) Copy
http://sourceforge.net/projects/socs/
Performs ungapped alignment of SOLiD (color space) sequencing reads against reference sequences.
Proper citation: SOCS (RRID:SCR_013223) Copy
http://sourceforge.net/projects/denovosolid/
Pipeline for small genome assembly using SOLiD sequencing technology.
Proper citation: DSP (RRID:SCR_013114) Copy
http://sourceforge.net/projects/tuxe/
Software that manages the RNA-sequencing pipeline based on the TopHat suite of software automatically.
Proper citation: Tuxedo (RRID:SCR_013194) Copy
http://seqtracs.sourceforge.net/
Software for a Laboratory Information Management System (LIMS) for tracking, organizing, and accessing sequencing requests and ABI trace files produced by a centralized sequencing core facility.
Proper citation: SeqTRACS (RRID:SCR_013294) Copy
http://bowtie-bio.sourceforge.net/crossbow/index.shtml
A scalable software pipeline for whole genome resequencing analysis.
Proper citation: Crossbow (RRID:SCR_013306) Copy
http://cliiq.sourceforge.net/Home
An algorithm to simultaneously identify and quantify expressed isoforms based on RNA-Seq data from multiple sample(s) in a population.
Proper citation: CLIIQ (RRID:SCR_009972) Copy
http://sourceforge.net/p/mira-assembler/wiki/Home/
Sequence assembler and mapper for whole genome shotgun and EST/RNASeq sequencing data.
Proper citation: MIRA (RRID:SCR_010731) Copy
http://sourceforge.net/projects/xdrawchem/
A drawing software application designed for drawing and analyzing chemical structures and reactions.
Proper citation: XDrawChem (RRID:SCR_010941) Copy
A software suite including a scalable hierarchical multitasking parallel infrastructure and the classical sequencing algorithms.
Proper citation: PPSEQ (RRID:SCR_010913) Copy
http://sourceforge.net/p/arpeggio/wiki/Home/
Software for harmonic compression of ChIP-seq data reveals protein-chromatin interaction signatures.
Proper citation: Arpeggio (RRID:SCR_010876) Copy
Digital repository software written in C# / ASP.net for powering digital libraries in a Windows server environment. Standards-based repository keeps all files in METS/MODS packages. Several related applications are available as well and the libraries can work independently as great digital library resources. SobekCM allows users to discover online resources via semantic and full-text searches, as well as a variety of different browse mechanisms. For each digital resource in the repository there are a plethora of display options, which may be selected by an appropriately authenticated use. This repository includes online metadata editing and online submissions in support of institutional repositories.
Proper citation: SobekCM (RRID:SCR_003225) Copy
http://mrsfast.sourceforge.net/
A cache-oblivious algorithm designed to map short reads to reference genome assemblies in a fast and memory-efficient manner. It optimizes cache usage to get higher performance. Currently Supported Features: * Mistmatches, No indels * Paired-end Mapping Mode * Discordant Paired-end Mapping Mode (to be used in conjuction with Variation Hunter)
Proper citation: mrsFAST (RRID:SCR_003128) Copy
http://splicq.sourceforge.net/
A Java software package which allows for the identification of splicing events and differentially expressed isoforms in next generation sequencing data.
Proper citation: SpliCQ (RRID:SCR_003266) Copy
http://sourceforge.net/projects/orfer/
An extended software package for high throughput PCR primer design for biological sequences. It reads the NCBI GenBank XML sequence format and extracts open reading frames for proteins. Sequences can be requested by GI or accession number.
Proper citation: ORFprimer (RRID:SCR_003269) Copy
http://sourceforge.net/projects/gemi/
Automated software tool to design polymerase chain reaction (PCR) primers. It accepts multiple aligned and long sequences with degenerated nucleotides. It can be used for quantitative/real-time PCR, conventional and Sanger sequencing. Gemi accepts DNA and RNA sequences with degenerate nucleotide (non-A/C/G/T bases). The programs are as the following: # The first program is to design PCR primers from multiple sequence alignment. # Program to convert ClustalW format (.aln), Phylip (.phy) and (.gde) formats to Fasta format. # Reverse and/or complement program is to find the reverse and complement counterpart of single or multiple sequences.
Proper citation: Gemi (RRID:SCR_003211) Copy
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