it looks like this tool is better than other assembler
http://seqanswers.com/forums/showthread.php?t=27470
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Member
Location: NY
Join Date: Feb 2009
Posts: 53
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 STAR: ultrafast universal RNA-seq aligner
Dear All,
I would like to formally introduce on SEQanswers our RNA-seq mapper STAR.
Its advantages include:
- Very high mapping speed:
on a modest 12-core cluster STAR maps 400 Million pairs per hour for human 2x100 Illumina reads (>50 times faster than TopHat).
- Accurate alignment of contiguous and spliced reads:
in our tests on real and simulated data STAR showed better sensitivity and precision than TopHat.
- Detection of polyA-tails, non-canonical splices and chimeric (fusion) junctions.
- Mapping reads of any length:
STAR can efficiently map reads of any length generated by current or emerging sequencing platforms, starting from ~15 bases (small RNA) and up to full length transcripts several kilobases long.
- Thorough testing on large ENCODE datasets:
STAR was used to map 64 Billion reads of long RNA-seq and 16 Billion reads of short RNA-seq, and will be used to map RNA-seq data in the next ENCODE phase.
STAR requires ~30GB of RAM for mapping to the human genome (could be reduced to 16GB in the "sparse" mode with some speed loss).
More information can be found in out recent paper.
If you decide to try it out, please download the latest STAR release.
I will be happy to answer any questions via SEQanswers, STAR discussion forum, or by e-mail: dobin@cshl.edu
Cheers
Alex |
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