A 3rd party evaluation of Ion Torrent's 316 chip data

Dan Koboldt (from massgenomics) has posted about what I know to be the 1st independent look at the data from Ion Torrent's 316 chip,
Granted the data was handed to him in a 'shiny report with color images' but he has bravely ignored that to give an honest look at the raw data itself.

The 316 chip gives a throughout that  nicely covers WGS reseq experiments for bacterial sized genomes. "The E. coli reference genome totals about 4.69 Mbp. With 175 Mbp of data, the theoretical coverage is around 37.5-fold across the E. coli genome."

For those wary of dry reviews, fear not, easily comprehensible graphs are posted within!

read the full post here

Tips for de novo bacterial genome assembly

Found this handy article for  de novo bacterial genome assembly.

In Summary,

1. Filter reads
2. Use VelvetOptimiser Script
3. Use Bowtie to map back reads to finished assembly to validate