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Archived Comments for: Comparing de novo assemblers for 454 transcriptome data

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

    Sujai Kumar, University of Edinburgh

    19 September 2011

    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.