View Single Post
Old 06-25-2013, 08:37 AM   #2
Senior Member
Location: Boston area

Join Date: Nov 2007
Posts: 747

De novo or resequencing?

Probably shoot for >50X coverage minimum. Higher initial coverage will allow more aggressive trimming/filtering of reads.

I have not assembled Ion data for a while, but historically the homopolymer calling issue leads to assemblies rich in indels. Perhaps someday someone will write the equivalent of Quiver for Ion Torrent data, but that hasn't happened yet.

Quality of the assembly will also be significantly affected by GC content (expect issues in regions with extremes in GC content) and the nature of the repeats in the genome. Set your expectations appropriately; short read, short insert technologies such as Ion cannot routinely close bacterial genomes -- you need either very long reads (PacBio) or mate pairs to have good odds of doing that.
krobison is offline   Reply With Quote