Wikiomics:RNA-Seq: Difference between revisions
Darek Kedra (talk | contribs) |
Darek Kedra (talk | contribs) |
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==SOLiD data only== | ==SOLiD data only== | ||
=== SplitSeek | (untested) | ||
=== SplitSeek === | |||
http://solidsoftwaretools.com/gf/project/splitseek/ | http://solidsoftwaretools.com/gf/project/splitseek/ | ||
Revision as of 08:32, 1 July 2010
Mappers
Spliced Mappers (tested)
Tophat
current version: 1.0.13 (BETA) from 2/5/2010 base mapper: bowtie
SOAPals
http://soap.genomics.org.cn/soapals.html
current version: 1.1 , 05-05-2010
GEM
http://sourceforge.net/apps/mediawiki/gemlibrary/index.php?title=The_GEM_library
current version: GEM-binaries-Linux-x86_64-20100419-003425.tbz2 base mapper: GEM split-mapper
SOLiD data only
(untested)
SplitSeek
http://solidsoftwaretools.com/gf/project/splitseek/
current version: 1.3.2
RNA-mate
http://solidsoftwaretools.com/gf/project/rnamate
current version: 1.01
Spliced Mappers (in developement)
Mapsplice
http://www.netlab.uky.edu/p/bioinfo/MapSplice/ current version: 1.11 2010.5.18 base mapper: bowtie
Spliced Mappers (old)
ERANGE
http://woldlab.caltech.edu/rnaseq/
current version: 3.1 from 2009/04/17. base mapper: bowtie (see version restriction)
GMORSE
http://www.genoscope.cns.fr/externe/gmorse/ Proper name: G-Mo.R-Se current version: 06-Nov-2009
It was used for Vitis vinifera genome project.
Not spliced
Mapping short reads to draft genome sequence with multiple contigs poses problems for current spliced mappers.
blat
http://genome.ucsc.edu/FAQ/FAQblat.html
last
http://last.cbrc.jp/ Latest: last-119.zip 18-May-2010
