title: Improved variation calling via an iterative backbone remapping and local assembly method for bacterial genomes.
abstract: Sequencing data analysis remains limiting and problematic, especially for low complexity repeat sequences and transposon elements due to inherent sequencing errors and short sequence read lengths. We have developed a program, ReviSeq, which uses a hybrid method composed of iterative remapping and local assembly upon a bacterial sequence backbone. Application of this method to six Brucella suis field isolates compared to the newly revised B. suis 1330 reference genome identified on average 13, 15, 19 and 9 more variants per sample than STAMPY/SAMtools, BWA/SAMtools, iCORN and BWA/PINDEL pipelines, and excluded on average 4, 2, 3 and 19 variants per sample, respectively. In total, using this iterative approach, we identified on average 87 variants including SNVs, short INDELs and long INDELs per strain when compared to the reference. Our program outperforms other methods especially for long INDEL calling. The program is available at http://reviseq.sourceforge.net.
authors.affiliation: Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, USA.
authors.forename: Hongseok
authors.initials: H
authors.lastname: Tae
authors.forename: Robert E
authors.initials: RE
authors.lastname: Settlage
authors.forename: Shamira
authors.initials: S
authors.lastname: Shallom
authors.forename: Jasmin H
authors.initials: JH
authors.lastname: Bavarva
authors.forename: Dale
authors.initials: D
authors.lastname: Preston
authors.forename: Gregory N
authors.initials: GN
authors.lastname: Hawkins
authors.forename: L Garry
authors.initials: LG
authors.lastname: Adams
authors.forename: Harold R
authors.initials: HR
authors.lastname: Garner
mesh_terms: D001483:Base Sequence; D041021:Brucella suis / Q000235:genetics*; D016000:Cluster Analysis; D005821:Genetic Techniques; D014644:Genetic Variation; D016680:Genome, Bacterial / Q000235:genetics*; D054643:INDEL Mutation / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software