Email updates

Keep up to date with the latest news and content from BMC Genomics and BioMed Central.

Open Access Highly Accessed Research article

Comparing de novo assemblers for 454 transcriptome data

Sujai Kumar and Mark L Blaxter*

BMC Genomics 2010, 11:571  doi:10.1186/1471-2164-11-571

PubMed Commons is an experimental system of commenting on PubMed abstracts, introduced in October 2013. Comments are displayed on the abstract page, but during the initial closed pilot, only registered users can read or post comments. Any researcher who is listed as an author of an article indexed by PubMed is entitled to participate in the pilot. If you would like to participate and need an invitation, please email info@biomedcentral.com, giving the PubMed ID of an article on which you are an author. For more information, see the PubMed Commons FAQ.

Using Newbler 2.5 (or 2.6) with -cdna and -utr

Sujai Kumar   (2011-09-19 14:23)  University of Edinburgh

For transcriptome data, Newbler has had a -cdna option since version 2.3 that makes "isotigs" and "isogroups".

However, since version 2.5(p1), there has been a -urt option as well which is recommended as a way of recovering low coverage transcripts (documented in detail in the manual for version 2.6) - and that is why we recommended using Newbler 2.5 with the -urt option in our paper.

We have been recommending Newbler 2.5 to our collaborators. I have heard of other researchers saying Newbler 2.5 (and now 2.6) didn't work as well as we said it would. However, in all those cases, the -urt option had not been used either.

So we are trying to figure out if some researchers are getting poorer results with Newbler despite using the -urt option, in which case we will stop recommending the use of Newbler to our collaborators. Post a comment here or let us know... Thanks!

Competing interests

I'm an author on this paper.

top

Post a comment