Greetings Hive Brain,
I am having issues with mapping reads of Streptococcus suis to the RefSeq genome. When I use it was a reference I only get about 30% of the reads mapping to it. When I do a de novo build I get the expect number of base pairs and when I blast the contigs they come back as Strep suis.
I know the streptococcus pneumoniae has a lot of internal rearrangement and I suspect that s.suis does as well, has anyone had any experiecne with either organisum and would be willing to give me any advice for assembly.
I'm using Ion torrent single end data, average fragment size is 280bp.