Hello, On 14/06/13 01:00 PM, Labo Derome wrote: > Hi, > To the analysis of SNPs, I need a file with the reads aligned on contigs, in > assembly with meta-ray, I tried with the command option " -amos" >but the resulting file does not seem that I need, what option can I use to >get a file with reads on contigs.
An AMOS file -- such as the one generated by Ray -- is best suited for visualization using high-end tools such as Tablet [1] or Hawkeye [2]. If what you desire is a SAM file, you can align your reads on the contigs. I suppose there are some tools to explore genetic variation using a SAM file. Also, you can generate a kmers.txt file to visualize your metagenome graph with a viewer, such as Ray Cloud Browser [3]. I know at least 3 tools that can generate these graphs: Ray, ABySS, and cortex. Both Ray and ABySS can dump a file that is directly compatible. You need to use cortex_binary_reader [4] with cortex. If you want to read more on variation mining using graphs, see these 2 papers: De novo assembly and genotyping of variants using colored de Bruijn graphs http://www.nature.com/ng/journal/v44/n2/full/ng.1028.html Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly http://bioinformatics.oxfordjournals.org/content/28/14/1838 --- [1] http://bioinf.scri.ac.uk/tablet/ [2] http://sourceforge.net/apps/mediawiki/amos/index.php?title=Hawkeye [3] http://genome.ulaval.ca:10241/client/?map=0§ion=1®ion=3&location=0&depth=10 [4] https://github.com/noporpoise/cortex_binary_reader > > Thanks. ------------------------------------------------------------------------------ This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
