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) |
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| 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 |
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| Method | Reference | Web-site | |||
| Rnnotator | (Martin et al. 2010) | Email to vtdelapuente@lbl.gov |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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. |
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| 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 |
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| 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) | 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 |
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| 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 |
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| Method | Reference | Web-site | |||
| BASIS | (Zheng et al. 2009) | http://www-rcf.usc.edu/ |
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| 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 |
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| 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 | |||
Put all of those in context? Please, focus on your genome browser instead
Joking aside, I am fact doing exactly that (putting them in context) right now: evaluating these tools one by one to see what problems they can solve. (and importantly, which ones of them can actually be run without ‘incantations and goat sacrifices’ as someone said on Twitter)
Please keep us posted about what you find. You are doing lot of work with evaluating and bench-marking the tools, and I was not planning to go that far. I was thinking about writing on their algorithms, potential shortfalls and few other things – stuff that demystifies a completely new algorithm to someone who is trying it for the first time.
“TopHap” should be “tophat”.
Thanks James.
[...] Methods to study Event/Isoform Expression and Alternative Splicing from RNA-Seq [...]
We’ve updated the tables with methods here:
http://regulatorygenomics.upf.edu/Software/RNA-Seq_and_splicing/
Thanks Eduardo. Very nice work !!
We will update ours with links to you.