1. Using a k-mer length of 71 will _presumably_ not work very well because of sequencing errors. First do a test run at k=31.
2. Are your interleaved files properly generated ? sequence1/1 sequence1/2 sequence2/1 sequence2/2 sequence3/1 sequence3/2 Do you get anything in LibraryStatistics.txt ? On Thu, 2012-03-01 at 17:06 -0500, LIU wrote: > Hi There, > > I have been using Ray to de novo assembly. > > The input reads are a mix of illumina pair-end reads (this account for > 90%), illumina single-end reads and 454 single end reads. > > The command i used is > mpiexec -n 60 Ray \ > -i \ > /home/s4196896/mix_assembly/input/t15c15/gs1.shuffled.fasta.gz \ > -i \ > /home/s4196896/mix_assembly/input/t15c15/gs2.shuffled.fasta.gz \ > -i \ > /home/s4196896/mix_assembly/input/t15c15/gs3.shuffled.fasta.gz \ > -s \ > /home/s4196896/mix_assembly/input/t15c15/gs2.single.fasta.gz \ > -s \ > /home/s4196896/mix_assembly/input/t15c15/gs3.single.fasta.gz \ > -s \ > /home/s4196896/mix_assembly/input/t15c15/gs1.single.fasta.gz \ > -s \ > /home/s4196896/mix_assembly/input/radseq1.seeds.fasta \ > -s \ > /home/s4196896/mix_assembly/input/radseq_v2.fasta \ > -s \ > /work1/s4196896/454_assembly/raw_reads/all_genomic_reads.short.fasta > \ > -s \ > /work1/s4196896/454_assembly/raw_reads/all_genomic_reads.long.fasta \ > -o \ > 71 \ > -k \ > 71 > > The output shows that scaffolds and contigs are the same (same N50, > total number of bases and number of sequences etc.). > > This confused me. > > > I hope someone can help me out. > > Thanks in advance. > > Kind Regards, > -- > Huanle > > School of biological Sciences, UQ, QLD, AU ------------------------------------------------------------------------------ Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 _______________________________________________ Denovoassembler-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
