Methods to study Event/Isoform Expression and Alternative Splicing from RNA-Seq

The RegulatoryGenomics website posts and updates a comprehensive list of tools for RNA-Seq analysis.

This is their current version.

Spliced-mappers

Method

Reference

Web-site

TopHap

(Trapnell et al. 2009)

http://tophat.cbcb.umd.edu/

MapSplice

(Wang et al. 2010)

http://www.netlab.uky.edu/p/bioinfo/MapSplice

SpliceMap

(Auger et al. 2010)

http://www.stanford.edu/group/wonglab/SpliceMap/

HMMSplicer

(Dimon et al. 2010)

http://derisilab.ucsf.edu/index.php?software=105

TrueSight

(Li et al. 2012b)

http://bioen-compbio.bioen.illinois.edu/TrueSight/

SOAPsplice

(Huang et al. 2011)

http://soap.genomics.org.cn/soapsplice.html

PASSion

(Zhang et al. 2012)

https://trac.nbic.nl/passion

PALMapper

(Jean et al. 2010)

http://galaxy.raetschlab.org/

SplitSeek

(Ameur et al. 2010)

http://solidsoftwaretools.com/gf/project/splitseek

Supersplat

(Bryant et al. 2010)

http://mocklerlab-tools.cgrb.oregonstate.edu/

SeqSaw

(Wang et al. 2011)

http://bioinfo.au.tsinghua.edu.cn/software/seqsaw

MapNext

(Bao et al. 2009)

http://evolution.sysu.edu.cn/english/software/mapnext.htm

STAR

(Dobin et al. 2012)

http://gingeraslab.cshl.edu/STAR/

GSNAP

(Wu et al. 2010)

http://research-pub.gene.com/gmap/

QPALMA

(De Bona et al. 2008)

http://www.raetschlab.org/suppl/qpalma

OSA

(Hu et al. 2012)

http://omicsoft.com/osa/

 

De novo Transcript assembly methods

Method

Reference

Web-site

Rnnotator

(Martin et al. 2010)

Email to vtdelapuente@lbl.gov

Multiple-k/STM

(Surget-Groba et al. 2010)

http://www.surget-groba.ch/downloads/stm.tar.gz

OASES

(Schultz et al. 2012)

http://www.ebi.ac.uk/~zerbino/oases/

Abyss

(Birol et al. 2009)

http://www.bcgsc.ca/platform/bioinfo/software/abyss

TransAbyss

(Robertson et al. 2010)

http://www.bcgsc.ca/platform/bioinfo/software/

Trinity

(Grabherr et al. 2011)

http://TrinityRNASeq.sourceforge.net

OASES

(Schultz et al. 2012)

http://www.ebi.ac.uk/~zerbino/oases/

Kissplice

(Sacomoto et al. 2012)

http://alcovna.genouest.org/kissplice/

Genome-based methods not using annotation

Method

Reference

Web-site

G-Mo.R-Seq

(Denoeud et al. 2008)

http://www.genoscope.cns.fr/externe/gmorse/

TAU

(Filichkin et al. 2010)

http://mocklerlab-tools.cgrb.oregonstate.edu/

Scripture

(Guttman et al. 2010)

http://www.broadinstitute.org/software/Scripture/

Cufflinks

(Trapnell et al. 2010)

http://cufflinks.cbcb.umd.edu/

IsoLasso

(Li et al. 2011a)

http://www.cs.ucr.edu/~liw/isolasso.html

CEM

(Li et al. 2012a)

http://www.cs.ucr.edu/~liw/cem.html

NSMAP

(Xia et al. 2011)

https://sites.google.com/site/nsmapforrnaseq

Montebello

(Hiller et al. 2012)

http://www.stanford.edu/group/wonglab/Montebello/Montebello_0.8.tar.gz

Casper

(Rosell et al. 2012)

https://sites.google.com/site/rosselldavid/software

Quantification of events using gene annotations

Method

Reference

Web-site

RUM

(Grant et al. 2011)

http://www.cbil.upenn.edu/RUM/userguide.php

X-MATE

(Wood et al. 2011)

http://grimmond.imb.uq.edu.au/X-MATE/

MMES

(Wang et al. 2010b)

Email to Wang.Liguo@mayo.edu

SpliceTrap

(Wu et al. 2011)

http://rulai.cshl.edu/splicetrap/

Genome-based quantification of isoforms using gene annotations

Method

Reference

Web-site

rSeq

(Jiang et al. 2009)

http://www-personal.umich.edu/~jianghui/rseq/

rQuant

(Bohnert et al. 2009)

http://galaxy.raetschlab.org/

SOLAS

(Richard et al. 2010)

http://cmb.molgen.mpg.de/2ndGenerationSequencing/Solas/

MISO

(Katz et al. 2010)

http://genes.mit.edu/burgelab/miso/

FluxCapacitor

(Montgomery et al. 2010)

http://flux.sammeth.net/capacitor.html

IsoformEx

(Kim et al. 2011)

http://bioinformatics.wistar.upenn.edu/isoformex

IsoInfer

(Feng et al. 2012)

http://www.cs.ucr.edu/~jianxing/IsoInfer.html

iReckon

(Mezlini et al. 2012)

http://compbio.cs.toronto.edu/ireckon/

IQSeq

(Du et al. 2012)

http://archive.gersteinlab.org/proj/rnaseq/IQSeq/

RABT

(Roberts et al. 2011)

http://bio.math.berkeley.edu/cufflinks.

SLIDE

(Li et al. 2011b)

https://sites.google.com/site/jingyijli/SLIDE.zip

Isoform quantification using transcriptome annotations

Method

Reference

Web-site

RSEM

(Li et al. 2011c)

https://github.com/bli25wisc/RSEM/

IsoEM

(Nicolae et al. 2011)

http://dna.engr.uconn.edu/?page_id=105

NEUMA

(Lee et al. 2011)

http://neuma.kobic.re.kr.

BitSeq

(Glaus et al. 2012)

http://www.bioconductor.org/packages/2.11/bioc/html/BitSeq.html

MMSEQ

(Turro et al. 2011)

http://bgx.org.uk/software/mmseq.html

eXpress

(Roberts et al. 2013)

http://bio.math.berkeley.edu/eXpress/

Annotation-guided reconstruction (and quantification) of isoforms

Method

Reference

Web-site

MapAl

(Labaj et al. 2012)

http://www.bioinf.boku.ac.at/pub/MapAl/

SpliceGrapher

(Rogers et al. 2012)

http://SpliceGrapher.sf.net

RABT

(Roberts et al. 2011)

http://bio.math.berkeley.edu/cufflinks.

ExonMap/ JunctionWalk

(Seok et al. 2012)

NA

DRUT

(Mangul et al. 2012)

http://www.cs.gsu.edu/~serghei/?q=drut

SLIDE

(Li et al. 2011b)

https://sites.google.com/site/jingyijli/SLIDE.zip

Gaze

(Howe et al. 2002)

http://www.sanger.ac.uk/resources/software/gaze/

JigSaw

(Allen et al. 2005)

http://www.cbcb.umd.edu/software/jigsaw/

EVM

(Haas et al. 2008)

http://evidencemodeler.sourceforge.net/

Augustus

(Stanke et al. 2006a)

http://bioinf.uni-greifswald.de/augustus/

Evigan

(Liu et al. 2008)

http://www.seas.upenn.edu/~strctlrn/evigan/evigan.html

Event-based differential splicing

Method

Reference

Web-site

Alexa-Seq

(Griffith et al. 2010)

http://www.alexaplatform.org/alexa_seq/

MISO

(Katz et al. 2010)

http://genes.mit.edu/burgelab/miso/

DEXSeq

(Anders et al. 2012)

http://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html

MATS

(Shen et al. 2012)

http://rnaseq-mats.sourceforge.net/

DiffSplice

(Hu et al. 2012)

http://www.netlab.uky.edu/p/bioinfo/DiffSplice

SOLAS

(Richard et al. 2010)

http://cmb.molgen.mpg.de/2ndGenerationSequencing/Solas/

JuncBASE

(Brooks et al. 2011)

http://compbio.berkeley.edu/proj/juncbase/Home.html

JETTA

(Seok et al. 2012b)

http://igenomed.stanford.edu/~junhee/JETTA/rnaseq.html

SpliceSeq

(Ryan et al. 2012)

http://bioinformatics.mdanderson.org/main/SpliceSeq:Overview

Isoform-based differential splicing

Method

Reference

Web-site

BASIS

(Zheng et al. 2009)

http://www-rcf.usc.edu/liangche/software.html

Alexa-Seq

(Griffith et al. 2010)

http://www.alexaplatform.org/alexa_seq/

FDM

(Singh et al. 2012)

http://csbio-linux001.cs.unc.edu/nextgen/software/FDM

MISO

(Katz et al. 2010)

http://genes.mit.edu/burgelab/miso/

rDiff

(Stegle et al. 2012)

http://galaxy.raetschlab.org/

Cuffdiff 2

(Trapnell et al. 2012)

http://cufflinks.cbcb.umd.edu/

DSGSeq

(Wang et al. 2012)

http://bioinfo.au.tsinghua.edu.cn/software/DSGseq

Visualization of Alternative Splicing

Method

Reference

Web-site

Sahimi Plots (MISO)

(Katz et al. 2010)

http://genes.mit.edu/burgelab/miso/docs/sashimi.html

SpliceGrapher

(Rogers et al. 2012)

http://SpliceGrapher.sf.net

Savant (iReckon)

(Fiume et al. 2010)

http://genomesavant.com/savant/

RSEM (WIG files)

(Li et al. 2011c)

https://github.com/bli25wisc/RSEM/

DiffSplice

(Hu et al. 2012)

http://www.netlab.uky.edu/p/bioinfo/DiffSplice

ALEXA-seq viewer

(Griffith et al. 2010)

http://www.alexaplatform.org/alexa_seq/

SpliceSeq

(Ryan et al. 2012)

http://bioinformatics.mdanderson.org/main/SpliceSeq:Overview

(send comments/suggestions to eduardo.eyras@upf.edu)