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Old 07-30-2012, 01:35 PM   #1
LSC
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Location: stanford

Join Date: Jul 2012
Posts: 24
Smile LSC - a fast PacBio long read error correction tool.

Hello SEQanswers Community,

Further Info: http://www.stanford.edu/~kinfai/LSC/LSC.html

We at the Wong Lab have developed a new tool for error correction of PacBio data. It has been shown to be very sensitive and can improve PacBio reads to 5% error rate. In particular, it is very very fast. In total, it only takes 10 hours (8 threading) for ~ 200k subreads. And it only needs 10-15G hardisk space for temporary files.

In it's current form it supports PacBio reads and any type of short reads (from any NGS platforms). In the current version, you may need novoalign (single-thread version, free for academic community).

It is designed for the Linux platform. If you use another platform leave us a note and we'll see what we can do.

Instructions are on the website that is still not perfect yet, but if you are having any troubles don't hesitate to leave me a note here.

Please give it a try and let me know if you have any issues. We are actively developing this tool so we welcome all of your comments and concerns! Especially, we are trying to replace novoalgin by the other aligner, which can save 50% running time (5 hours in the example above). The ease of use is very important to us, so let us know if anything annoys you.

Last edited by LSC; 07-30-2012 at 02:11 PM.
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