This page summarizes RNA-seq related activities carried out by the NGS taskforce member groups.
Need a local expert on RNA-Seq? Maybe one of the following names can help you.
- Peter-Bram ‘t Hoen (LUMC)
- Marieke Simonis (Hubrecht/UMCU)
- Yanju Zhang (LUMC)
- PASSion: a pattern growth based algorithm for splice site detection from paired-end RNA-Seq reads.
Evaluation of RNA tools
Work performed by Irina Pulyakhina (LUMC)
|Tool||Which algorithm/tool is used for mapping||Does the tool detect canonical/non-canonical splice sites||Speed (reads mapped per hour on a single thread)||Sensitivity||Specificity||Does the tool use paired-end information||The most appropriate for the tool application||The weak parts of the tool||Last update of the source code||Is the tool able to detect multiple splice events per single read||Does the tool search fpr novel splicing sites||Is the tool multi-thread||Link to the paper|
|GSNAP||indexing the reference and the reads; looking for overlaps in two index tables||canonical and non-canonical splice junctions||500000||yes||pre-mRNA||prioritize intron alignments to exon alignments||23-03-2012||yes||yes||yes||article|
|HMMSplicer||bowtie (alignment) + hidden Markov model (detection of a splice junction)||canonical and non-canonical splice junctions||2.2 mln||yes||low-abundance transcripts, low sequence quality||25-11-2010||no||yes||no info||article|
|MapSplice||first segment exonic alignment, then segment spliced alignment, then segment assembly||canonical and non-canonical splice junctions||100 mln||yes||aligning splice junctions de novo||12/04/12||yes||yes||yes||article|
|PASSion||pattern-growth algorithm||canonical and non-canonical splice junctions||no info||yes||splicings mediating across chromosome gene fusion||12/01/11||yes||yes||yes||article|
|SpliceMap||half-read mapping, finding exonic hits, searching for junctions||canonical splice junctions||30 mln||yes||10/01/10||no||yes||no info||article|
|SplitSeek||mapping pieces of fragments of reads (anchors) and extending anchor alignments||canonical splice junction||no info||yes||Abi Solid reads||only Abi Solid reads||19-11-2010||no||yes||no||article|
|TopHat||bowtie + partitioning unmapped reads||canonical and non-canonical splice junctions||2.2 mln||yes||02/02/12||no||yes||yes||article|