title: Optimization and cost-saving in tagmentation-based mate-pair library preparation and sequencing.
abstract: In de novo genome sequencing, mate-pair reads are crucial for scaffolding assembled contigs. However, preparation of mate-pair libraries is not a trivial task, even when using one of the latest approaches, the Nextera Mate Pair Sample Prep Kit from Illumina. To reduce cost and enhance library yield and fidelity when using this kit, we have modified the manufacturer's protocol based on (i) variable tagmentation conditions, (ii) intensive DNA shearing to decrease library insert length, and (iii) sequencing on an Illumina HiSeq with >150 cycles. Finally, we provide additional suggestions for further improvement in the application of this kit.
authors.affiliation: Phyloinformatics Unit, RIKEN Center for Life Science Technologies, Kobe, Japan.
authors.forename: Kaori
authors.initials: K
authors.lastname: Tatsumi
authors.affiliation: Phyloinformatics Unit, RIKEN Center for Life Science Technologies, Kobe, Japan.
authors.forename: Osamu
authors.initials: O
authors.lastname: Nishimura
authors.affiliation: Phyloinformatics Unit, RIKEN Center for Life Science Technologies, Kobe, Japan.
authors.forename: Kazu
authors.initials: K
authors.lastname: Itomi
authors.affiliation: Phyloinformatics Unit, RIKEN Center for Life Science Technologies, Kobe, Japan.
authors.forename: Chiharu
authors.initials: C
authors.lastname: Tanegashima
authors.affiliation: Phyloinformatics Unit, RIKEN Center for Life Science Technologies, Kobe, Japan.
authors.forename: Shigehiro
authors.initials: S
authors.lastname: Kuraku
mesh_terms: D000818:Animals; D001483:Base Sequence; D004247:DNA / Q000032:analysis* / Q000235:genetics; D053938:DNA Fragmentation; D015723:Gene Library; D016678:Genome / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D008969:Molecular Sequence Data; D012104:Reptiles; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D004247:DNA
keywords: CEGMA; genome assembly; genome scaffolding; mate pair library; tagmentation