On 10/05/13 11:26 AM, Yuqing Xiong wrote: > Thank you very much. However, I have a question still. How did you know a > contig belongs to which species in metagenome assembly?
In our paper, we aligned all the assembled contigs to the set of sequences using MUMmer. We did not clasify contigs before alignment because MUMmer reports maximum unique matches. See Section "Validation of assemblies" in our paper [1]. --- [1] http://genomebiology.com/2012/13/12/R122 > > > On Fri, May 10, 2013 at 9:49 AM, Sébastien Boisvert > <[email protected] <mailto:[email protected]>> > wrote: > > On 08/05/13 05:33 PM, Yuqing Xiong wrote: > > Hi, Sebastien, > > I am a researcher in computational biology, and studying your > papers,"Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput > Sequencing Technologies" > and "Ray Meta: scalable de novo metagenome assembly and profiling". > The former is about non metagenome assembly and the latter is about > metagenome assembly. > When the quality of the assemblies are assessed, the assembly metrics > at the two paper are different, the chimeric contig, mismatch, and indel are > included > at the former, but not inculded at the latter. I think that the cause > is from binning, that is, it is not known that a contig belongs to which > species in metagenome assembly. > > My question is that why you don't confirm every contig belong to > which species, and then assess the quality of assembly of every contig in the > second paper? > > > We actually verified the assembly quality in our paper [1] for the > 100-genome metagenome and for the 1000-genome > metagenome (in the Results section). > > Best regards, > > --Yuqing > > > > --- > [1] http://genomebiology.com/2012/__13/12/R122 > <http://genomebiology.com/2012/13/12/R122> > > ------------------------------------------------------------------------------ Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may _______________________________________________ Denovoassembler-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
