SAM/BAM: It’s time for a single standard for assembly output
Just what the title says really. A quick note after kicking around this issue with Peter Cock and the Tablet team. We need a single standard for assembly output. I don’t really care what it is. But it should be SAM/BAM. Why? Easy. This is already the de facto standard for mapping alignments. It’s actively [...]
Assembling Illumina and 454 data
This is a question that keeps cropping up on Seqanswers and Biostar. Amazingly there is still no 100% satisfactory pipeline for assembling combined Illumina and 454 data de novo. Here are the ways I know about: 1) Assemble 454 data on its own and correct with Illumina data For example, Newbler for the 454 data. [...]
Ion Torrent data blog post; a week is a long time in genomics
My last blog post looking at de novo assembly with Ion Torrent did over 2,000 views (a big number in these parts) and shows what huge interest there is in Ion Torrent data. Despite my protestations that this was not an assembly software comparison, a few people took it that way. I guess that’s natural. [...]
Genome sequencing platforms compared for bacterial de novo assemblies
Wow, I haven’t blogged for ages. Partly this is the usual excuse of not having time, and partly a lack of inspiration. Sorry. Perhaps just before Xmas is the wrong time to get my mojo back, but I guess that’s the way life is. So what’s been happening? Well, on the sequencing front we’ve recently [...]