Yes. Ray will use single-end reads as paths in the de Bruijn graph and paired-end or mate-pair reads as pairs of paths in the de Bruijn graph.
Furthermore, all the reads contribute to the k-mers of the graph. On Fri, 2012-03-16 at 18:39 -0700, habibr wrote: > Will Ray also use the SE reads for the assembly in addition to the PE reads? > > 2012/3/16 Sébastien Boisvert < > re...@reply.github.com > > > > > Yes. > > > > You will get something like this for library statistics with 2 sets of > > pairs (like in your example): > > > > [megaman@rohan PrettyGood-2012-03-11]$ less ERS006509 > > +Ray-2012-03-11-Mithrandir/Assembly/LibraryStatistics.txt > > > > NumberOfPairedLibraries: 2 > > > > LibraryNumber: 0 > > InputFormat: TwoFiles,Paired > > DetectionType: Automatic > > File: Sample/ERR011301_1.fastq.gz > > NumberOfSequences: 12786171 > > File: Sample/ERR011301_2.fastq.gz > > NumberOfSequences: 12786171 > > Distribution: Assembly/Library0.txt > > Peak 0 > > AverageOuterDistance: 136 > > StandardDeviation: 7 > > > > LibraryNumber: 1 > > InputFormat: TwoFiles,Paired > > DetectionType: Automatic > > File: Sample/ERR011302_1.fastq.gz > > NumberOfSequences: 8850301 > > File: Sample/ERR011302_2.fastq.gz > > NumberOfSequences: 8850301 > > Distribution: Assembly/Library1.txt > > Peak 0 > > AverageOuterDistance: 349 > > StandardDeviation: 18 > > > > > > > > > > On Thu, 2012-03-15 at 21:09 -0700, habibr wrote: > > > Hi Sebastien, > > > > > > is it possible to use Ray on several PE reads plus SE reads? > > > For example, Ray -p A_R1.fastq A_R2.fastq -p B_R1.fastq B_R2.fastq -s > > A_SE.fastq -s B_SE.fastq ? > > > > > > Habib > > > > > > -- > > > Reply to this email directly or view it on GitHub: > > > http://github.com/inbox/36050990#reply > > > > -- > > Reply to this email directly or view it on GitHub: > > http://github.com/inbox/36050990#reply > > > > > ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
