From: Ole K. T. <o.k...@bi...> - 2012-01-20 14:10:15
|
Hi, I want to run amosvalidate on different assemblies generated by different assemblers. It's easy to convert from Newbler and Celera to an AMOS bank, but I'm also interested in looking at the output from ALLPATHS-LG, SOAPdenovo, SGA, etc.. I guess one general way of doing this is to align all the reads to the finished assembly via BWA/Bowtie, but then a SAM/BAM to AMOS bank converter is needed. Does anyone know of something like this, or any other way of doing this? It seems that someone might have worked on a BAM to AMOS converter during the summer (http://sourceforge.net/mailarchive/forum.php?thread_name=C05E1437EB0B4E0FA990BCFED31F784E%40ewoks&forum_name=amos-help: "The newest version of samtools / IGV / etc have proper support of gapped alignments. My understanding is someone from UMD will be working on BAM to AMOS converters this summer, but I don't know the is an exact timeline."), but I can't find anything else about it. Sincerely, Ole Kristian Tørresen |