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Forum: Pacific Biosciences 09-20-2012, 01:39 PM
Replies: 31
Views: 13,510
Posted By tplsmith
Some input about error correction

We have been working with Sergey on the PacBioToCA for some time. First, you can definitely have too much coverage of short reads, especially illumina reads where errors are non-random and can...
Forum: Bioinformatics 05-01-2012, 05:35 AM
Replies: 1
Views: 3,306
Posted By tplsmith
The new v1.3 release from PacBio supposedly...

The new v1.3 release from PacBio supposedly supports hybrid assembly, I have not made much attempt to get it to work since we had already implemented a pipeline based on the PacBioToCA plug-in for...
Forum: Bioinformatics 05-01-2012, 05:27 AM
Replies: 3
Views: 4,949
Posted By tplsmith
There is a plug-in of the latest Celera...

There is a plug-in of the latest Celera assembler, PacBioToCA, written by Sergey Koren at NBACC, that uses illumina reads to error-correct PacBio reads and outputs a frg file for OLC assembly in the...
Forum: 454 Pyrosequencing 08-06-2010, 12:28 PM
Replies: 21
Views: 11,733
Posted By tplsmith
There is clearly a reagent problem with emPCR...

There is clearly a reagent problem with emPCR reagents of late. Even libraries that we have previously run do not perform well using recent lots of SV emPCR reagents. This is less true of LV emPCR...
Forum: Bioinformatics 08-03-2010, 11:05 AM
Replies: 6
Views: 5,984
Posted By tplsmith
MIRA-based pipeline to view scaffolds

Not sure what you really want is to "combine" a reference and your de novo stuff. Researchers that I have been assisting in the same kinds of studies have had good success using the MIRA assembler...
Forum: RNA Sequencing 07-01-2010, 12:09 PM
Replies: 2
Views: 2,540
Posted By tplsmith
RNA ppt vs SPRI or MinElute

Either SPRI or MinElute frequently lower your yield; if RNA is not limiting this is not a problem. Recommend that you have calibrated your SPRI beads if they are XP as there is slight risk of...
Forum: Introductions 06-29-2010, 08:26 AM
Replies: 373
Views: 118,660
Posted By tplsmith
Greetings from rural Nebraska. I am hapless...

Greetings from rural Nebraska. I am hapless director of sequencing facility with an aging 454 and 3730s, trying to merge data with HiSeq from another facility. Also expectant parent to a PacBio...
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