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http://weizhong-lab.ucsd.edu/rammcap/cgi-bin/rammcap.cgi
Metagenomic software pipeline for analysis and comparison of very large metagenomes with fast clustering and functional annotation.
Proper citation: RAMMCAP (RRID:SCR_011927) Copy
https://www.genome-cloud.com/user/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 29, 2019. A cloud platform for next-generation sequencing analysis and storage. Services include: * g-Analysis: Automated genome analysis pipelines at your fingertips * g-Cluster: Easy-of-use and cost-effective genome research infrastructure * g-Storage: A simple way to store, share and protect data * g-Insight: Accurate analysis and interpretation of biological meaning of genome data
Proper citation: GenomeCloud (RRID:SCR_011886) Copy
http://euler.bc.edu/marthlab/scotty/scotty.php/
A tool to assist in the designing of RNA Seq experiments that have adequate power to detect differential expression at the level required to achieve experimental aims.
Proper citation: Scotty (RRID:SCR_011889) Copy
http://www.cs.ucr.edu/~jianxing/IsoInfer.html
A C/C++ program to infer isoforms based on short RNA-Seq (single-end and paired-end) reads, exon-intron boundary and TSS/PAS information.
Proper citation: IsoInfer (RRID:SCR_011892) Copy
Software tool that enables analysis of RNA-seq data with or without reference genome. Local transcriptome assembler for SNPs, indels and AS events.
Proper citation: KisSplice (RRID:SCR_011893) Copy
http://bioinformatics.childhealthresearch.org.au/software/fusionfinder/
A perl-based software package, which can be used to find fusion transcript candidates in RNA-Seq data.
Proper citation: FusionFinder (RRID:SCR_011894) Copy
http://uc-echo.sourceforge.net/
Error correction algorithm designed for short-reads from next-generation sequencing platforms such as Illumina''s Genome Analyzer II.
Proper citation: ECHO (RRID:SCR_011851) Copy
http://calpain.org/predict.rb?cls=substrate
Calpain cleavage prediction using multiple kernel learning.
Proper citation: CaMPDB (RRID:SCR_011976) Copy
A community created to advance the use and value of next-generation sequencing through knowledge sharing.
Proper citation: NGS Leaders (RRID:SCR_011982) Copy
A desktop application for the bench biologists to analyse RNA-Seq and microarray expression data. It performs gene-centric analyses such as differential expression and pathways using well-established R modules, integrates data from multiple sources, and enables editing of R commands., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Guide (RRID:SCR_011903) Copy
http://www.unav.es/genetica/oncofuse.html
Software tool designed to predict the oncogenic potential of fusion genes found by Next-Generation Sequencing in cancer cells.
Proper citation: Oncofuse (RRID:SCR_011904) Copy
http://bioinformatics.mdanderson.org/main/PRADA:Overview
A pipeline to analyze paired end RNA-Seq data to generate gene expression values (RPKM) and gene-fusion candidates.
Proper citation: PRADA (RRID:SCR_011906) Copy
https://mcdonaldlab.biology.gatech.edu/r-sap/
An automated bioinformatics pipeline that analyzes and quantitates high-throughput RNA-Seq datasets.
Proper citation: R-SAP (RRID:SCR_011907) Copy
http://mapman.gabipd.org/web/guest/robin
Software package for RNA-Seq-based transcriptomics. Used to analyse Illumina/Solexa-based RNA-Seq data, Affymetrix data and generic tabular two color or single channel array data. Offers variety of quality control methods that can be used to gain overview of experimental data technical quality and structure.
Proper citation: RobiNA (RRID:SCR_011908) Copy
https://code.google.com/p/rseqflow/
An RNA-Seq analysis pipeline which offers an express implementation of analysis steps for RNA sequencing datasets.
Proper citation: RseqFlow (RRID:SCR_011909) Copy
https://code.google.com/p/seqpipe/
A command line-based pipeline framework for bioinformatics research.
Proper citation: SeqPipe (RRID:SCR_011862) Copy
http://1001genomes.org/software/shore.html
A mapping and analysis pipeline for short read data produced on the Illumina platform.
Proper citation: SHORE (RRID:SCR_011863) Copy
A question and answer site for professional and enthusiast programmers.
Proper citation: Stack Overflow (RRID:SCR_011984) Copy
Open Access Bioinformatics resource portal.
Proper citation: Bioinformaticsweb (RRID:SCR_011988) Copy
http://wwwdev.ebi.ac.uk/fg/hts_mappers/
Data set providing an up-to-date compendium of HTS mappers initially provided in the article Tools for mapping high-throughput sequencing data. Please let fill out the provided form if you are a developer and your mapper is not listed or you want to update the data for your mapper.
Proper citation: HTS Mappers (RRID:SCR_011991) Copy
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