title: Genomer--a Swiss army knife for genome scaffolding.
abstract: The increasing accessibility and reduced costs of sequencing has made genome analysis accessible to more and more researchers. Yet there remains a steep learning curve in the subsequent computational steps required to process raw reads into a database-deposited genome sequence. Here we describe "Genomer," a tool to simplify the manual tasks of finishing and uploading a genome sequence to a database. Genomer can format a genome scaffold into the common files required for submission to GenBank. This software also simplifies updating a genome scaffold by allowing a human-readable YAML format file to be edited instead of large sequence files. Genomer is written as a command line tool and is an effort to make the manual process of genome scaffolding more robust and reproducible. Extensive documentation and video tutorials are available at http://next.gs.
authors.affiliation: Biology Department, The University of Akron, Akron, Ohio, United States of America. mail@michaelbarton.me.uk
authors.forename: Michael D
authors.initials: MD
authors.lastname: Barton
authors.forename: Hazel A
authors.initials: HA
authors.lastname: Barton
mesh_terms: D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D058977:Molecular Sequence Annotation; D012984:Software