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http://ftp://ftp.pasteur.fr/pub/gensoft/projects/AlienTrimmer/
Allows detecting and removing multiple alien sequences in both ends of sequence reads.
Proper citation: AlienTrimmer (RRID:SCR_011835) Copy
https://github.com/najoshi/sabre
Software tool to demultiplex barcoded reads into separate files. Works on both single-end and paired-end data in fastq format. Used in next generation sequencing to analyze a broad range of data.
Proper citation: sabre (RRID:SCR_011843) Copy
http://www.scbi.uma.es/ingebiol/session/new/seqtrimnext
A customizable and distributed pre-processing software for NGS (Next Generation Sequencing) biological data.The old version for Sanger sequences, Seqtrim, has been discontinued.
Proper citation: SeqtrimNEXT (RRID:SCR_011845) Copy
http://www.ebi.ac.uk/~zerbino/oases/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool as de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly.
Proper citation: Oases (RRID:SCR_011896) Copy
http://tophat.cbcb.umd.edu/fusion_index.html
An algorithm for Discovery of Novel Fusion Transcripts with the ability to align reads across fusion points, which results from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome.
Proper citation: TopHat-Fusion (RRID:SCR_011899) Copy
http://cbcb.umd.edu/software/metAMOS
A modular and open source metagenomic assembly and analysis pipeline.
Proper citation: MetAMOS (RRID:SCR_011914) Copy
http://genome.ucsc.edu/cgi-bin/hgBlat?command=start
Software designed to quickly find sequences of 95% and greater similarity of length 25 bases or more.
Proper citation: BLAT (RRID:SCR_011919) Copy
http://www.bios.unc.edu/research/genomic_software/BBSeq/
A Powerful and Flexible Approach to the Analysis of RNA Sequence Count Data.
Proper citation: BBSeq (RRID:SCR_011877) 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://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://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
Web based instant protein network modeler for newly sequenced species. Web server designed to instantly construct genome scale protein networks using protein sequence data. Provides network visualization, analysis pages and solution for instant network modeling of newly sequenced species.
Proper citation: JiffyNet (RRID:SCR_011954) Copy
http://www.optimaldesign.com/ArrayMiner/ArrayMiner.htm
A set of analysis tools using advanced algorithms to reveal the true structure of your gene expression data.
Proper citation: ArrayMiner (RRID:SCR_011955) Copy
http://sourceforge.net/projects/mirplant/
A user-friendly plant miRNA prediction tool.
Proper citation: miRPlant (RRID:SCR_012105) Copy
https://code.google.com/p/slidesort-bpr/
Software using a reference-free method for detecting clusters of breakpoints from the chromosomal rearrangements.
Proper citation: SlideSort-BPR (RRID:SCR_012079) Copy
http://www.bioinf.jku.at/software/fabia/fabia.html
A model-based technique for biclustering that is clustering rows and columns simultaneously.
Proper citation: FABIA (RRID:SCR_012002) Copy
Software that allows fast and user-friendly verification of Mascot result files, as well as data quantification using isotopic labeling methods (SILAC/ICAT) or label free approaches (spectral counting, MS signal comparison).
Proper citation: MFPaQ (RRID:SCR_012049) Copy
http://sourceforge.net/projects/multiplierz/
An open-source Python-based environment that provides a scriptable framework for efficient access to manufacturers'' proprietary data files via mzAPI.
Proper citation: multiplierz (RRID:SCR_012058) Copy
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