Methods to study Event/Isoform Expression and Alternative Splicing from

RegulatoryGenomics website posts and updates a comprehensive list of tools for RNAseq analysis, and the current version is posted below. If you are overwhelmed with too many tools, please wait till our next commentary, where we will put them all in context. Also check this seqanswers thread for more on the topic.

(please send

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

Spliced-mappers

Method

Reference

Web-site

TopHat

(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

MapAI

(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)

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)

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