We received an email from Anton Korobeynikov of Algorithmic Biology Lab about the release of SPAdes 3.0. Anton mentioned several months back that they were working to incorporate PacBio reads in hybrid mode, and now it is official !! You can download the software from here and the list of changes are given below.
We look forward to reading the manuscript that presents their algorithms. Anton told us that they are working on it, but if it does not come too soon, we have to start poking around the code :)
SPAdes 3.0.0, 29 December 2013
NEW: Module for assemblying diplod highly polymorphic genomes.
NEW: Support for PacBio reads.
NEW: Support for IonTorrent reads.
NEW: Support for Sanger reads and additional contigs.
NEW: Possibility to restart SPAdes starting from the specified check-point with the –restart-from option.
NEW: Output contigs/scaffolds in FASTA and FASTG.
CHANGE: Improved algorithm for mate-pair repeat resolution and scaffolding.
CHANGE: Improved N50 and misassembly rate for single-cell data sets with low genome fraction.
FIX: User-friendly handling for errors in mismatch corrector.
REMOVE: Rectangle graph repeat resolution module.