Nextera mate pairs sample prep kit

In addition to the sequencing libraries reported in Burke et al. (2014) (link) (180 bp, 1.5 kb, 5 kb, and 10 kb), a new 20 kb long-insert mate-pair library was constructed from pooled adult male DNA using Illumina’s Nextera Mate-Pairs Sample Prep Kit. All libraries were sequenced for 100 cycles on a HiSeq2000 using TruSeq chemistry. Raw reads were trimmed, filtered, and error-corrected as described in Burke et al. (2014) (link). The Mdem1 assembly was further improved by additional scaffolding with the 20 kb Nextera mate-pair library and use of GapCloser v1.12 to close gaps generated in the scaffolding process with short paired read data (Luo et al. 2012 (link)). The genome assembly was screened by NCBI during the whole genome submission process to filter out adapter, vector, and other contaminant sequences. Methods used to generate RNASeq and viral DNA libraries and sequence data used for mapping have been described previously (Bitra et al. 2016 (link); Burke and Strand 2014 (link); Burke et al. 2014 (link); Burke and Strand 2012; Burke 2016 (link)).