Comparative assessment of methods for computational inference of transcript isoform from RNA-seq data

Benchmarked Methods



Name Alignment to Transcript information Year of release Link Pubmed Id
BitSeqTranscriptomeSequences2012http://bitseq.github.io/24413218, 22563066
CEMGenomeAnnotations2012http://alumni.cs.ucr.edu/~liw/cem.html23060617
CufflinksGenomeAnnotations2010http://cole-trapnell-lab.github.io/cufflinks/20436464
eXpressTranscriptomeSequences2012//bio.math.berkeley.edu/eXpress/index.html23160280
IsoEMGenomeAnnotations2011http://dna.engr.uconn.edu/?page_id=10521504602
MMSEQTranscriptomeSequences2011https://github.com/eturro/mmseq21310039
RSEMTranscriptomeSequences2009http://deweylab.biostat.wisc.edu/rsem/20022975, 21816040
rSeqTranscriptomeSequences2009http://www-personal.umich.edu/~jianghui/rseq/19244387
SailfishN/ASequences2014http://www.cs.cmu.edu/~ckingsf/software/sailfish/24752080
ScriptureGenomeAnnotations2010https://www.broadinstitute.org/software/scripture/20436462
TIGAR2TranscriptomeSequences2013https://github.com/nariai/tigar223821651, 25560536