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http://primerseq.sourceforge.net/
Software that designs RT-PCR primers that evaluate alternative splicing events by incorporating RNA-Seq data. It is particularly advantageous for designing a large number of primers for validating alternative splicing events found in RNA-Seq data. It incorporates RNA-Seq data in the design process to weight exons by their read counts. Essentially, the RNA-Seq data allows primers to be placed using actually expressed transcripts. This could be for a particular cell line or experimental condition, rather than using annotations that incorporate transcripts that are not expressed for the data. Alternatively, you can design primers that are always on constitutive exons. PrimerSeq does not limit the use of gene annotations and can be used for a wide array of species.
Proper citation: PrimerSeq (RRID:SCR_003295) Copy
http://sourceforge.net/projects/seqexpress/
A cross-platform software that estimates gene/isoform expression level via mRNA-Seq data. SeqExpress exams the Sequencing bias in mRNA-Seq and correct it to get more accurate estimation.
Proper citation: SeqExpress (RRID:SCR_004013) 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/vanator-cvr/
A Perl pipeline utilising a large variety of common alignment, assembly and analysis tools to assess the metagenomic profiles of Illumina deep sequencing samples. The emphasis is on the discovery of novel viruses in clinical and environmental samples.
Proper citation: Vanator (RRID:SCR_004370) Copy
http://sourceforge.net/projects/taipan/
A fast hybrid short-read assembly tool.
Proper citation: Taipan (RRID:SCR_007330) Copy
http://genotan.sourceforge.net/
A free software tool to identify length variation of microsatellites from short sequence reads.
Proper citation: GenoTan (RRID:SCR_007935) Copy
A cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data.
Proper citation: BRIG (RRID:SCR_007802) Copy
http://seqpig.sourceforge.net/
A software library for Apache Pig for the distributed analysis of large sequencing datasets on Hadoop clusters.
Proper citation: SeqPig (RRID:SCR_008548) Copy
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
http://scalce.sourceforge.net/Home
A FASTQ compression tool that uses locally consistent parsing to obtain better compression rate.
Proper citation: SCALCE (RRID:SCR_009658) Copy
http://sourceforge.net/projects/phaccs/
Software that gives estimates of the structure and diversity of uncultured viral communities using metagenomic information.
Proper citation: PHACCS (RRID:SCR_001232) Copy
Quality assessment software tool for evaluating and comparing genome assemblies. It works both with and without a given reference genome. It produces many reports, summary tables and plots.
Proper citation: QUAST (RRID:SCR_001228) Copy
http://sourceforge.net/projects/kanalyze/
A Java toolkit designed to convert DNA and RNA sequences into k-mers.
Proper citation: KAnalyze (RRID:SCR_001323) Copy
http://sourceforge.net/projects/baccontigeditor/
A simple sequence alignment editing tool, written in Java.
Proper citation: BACContigEditor (RRID:SCR_001617) Copy
http://sourceforge.net/projects/dnaclust/
Software program for clustering large number of short similar DNA sequences. It was originally designed for clustering targeted 16S rRNA pyrosequencing reads.
Proper citation: DNACLUST (RRID:SCR_001771) Copy
http://biolemmatizer.sourceforge.net/
A domain-specific lemmatization software tool for the morphological analysis of biomedical literature.
Proper citation: BioLemmatizer (RRID:SCR_000117) Copy
http://soap.genomics.org.cn/soapfuse.html
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on August 23,2022. An open source tool developed for genome-wide detection of fusion transcripts from human being paired-end RNA-Seq data. This tool is a part of a larger set of tools to efficiently align oligonucleotides onto reference sequences .
Proper citation: SOAPfuse (RRID:SCR_000078) Copy
http://sourceforge.net/projects/exomesuite/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software application designed to analyze variant call files from next generation sequencing data to identify variants causing disease.
Proper citation: exomeSuite (RRID:SCR_000129) Copy
https://github.com/lskatz/cg-pipeline
A software tool for assembling genome sequence data and running feature prediction and annotation tools on the assembly.
Proper citation: CG-Pipeline (RRID:SCR_000047) Copy
http://sourceforge.net/projects/batman-seq/
A fast BWT-based short reads mapping tools which uses additional statistical method to model error profile of the sequencing experiment.
Proper citation: Batman-Seq (RRID:SCR_000048) Copy
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