title: Finishing bacterial genome assemblies with Mix.
abstract: BACKGROUND
  Among challenges that hamper reaping the benefits of genome assembly are both unfinished assemblies and the ensuing experimental costs. First, numerous software solutions for genome de novo assembly are available, each having its advantages and drawbacks, without clear guidelines as to how to choose among them. Second, these solutions produce draft assemblies that often require a resource intensive finishing phase.
  
  
  METHODS
  In this paper we address these two aspects by developing Mix , a tool that mixes two or more draft assemblies, without relying on a reference genome and having the goal to reduce contig fragmentation and thus speed-up genome finishing. The proposed algorithm builds an extension graph where vertices represent extremities of contigs and edges represent existing alignments between these extremities. These alignment edges are used for contig extension. The resulting output assembly corresponds to a set of paths in the extension graph that maximizes the cumulative contig length.
  
  
  RESULTS
  We evaluate the performance of Mix on bacterial NGS data from the GAGE-B study and apply it to newly sequenced Mycoplasma genomes. Resulting final assemblies demonstrate a significant improvement in the overall assembly quality. In particular, Mix is consistent by providing better overall quality results even when the choice is guided solely by standard assembly statistics, as is the case for de novo projects.
  
  
  BACKGROUND
  Mix is implemented in Python and is available at https://github.com/cbib/MIX, novel data for our Mycoplasma study is available at http://services.cbib.u-bordeaux2.fr/mix/.
authors.forename: Hayssam
authors.initials: H
authors.lastname: Soueidan
authors.forename: Florence
authors.initials: F
authors.lastname: Maurier
authors.forename: Alexis
authors.initials: A
authors.lastname: Groppi
authors.forename: Pascal
authors.initials: P
authors.lastname: Sirand-Pugnet
authors.forename: Florence
authors.initials: F
authors.lastname: Tardy
authors.forename: Christine
authors.initials: C
authors.lastname: Citti
authors.forename: Virginie
authors.initials: V
authors.lastname: Dupuy
authors.forename: Macha
authors.initials: M
authors.lastname: Nikolski
mesh_terms: D000465:Algorithms; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D009174:Mycoplasma / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods; D012985:Software Design