PacBio SMRT DNA Sequencing and Assembly

Libraries for sequencing were prepared according to the Pacific Biosciences (PacBio) protocol, and sequencing was performed at the Arizona Genomics Institute (AGI; Tucson, USA) using a SMRT DNA sequencing system available from PacBio (PacBio RSII platform). The sequences were deposited into the NCBI SRA databank under bioproject number PRJNA647392. De novo assembly was performed with the PacBio Corrected Reads (PBcR) pipeline implemented as part of Wgs-assembler v8.3rc2 [48 (link)] and Celera Assembler [49 (link)]. The contigs obtained with the assemblers were subjected to error correction with pbalign (v0.2). The PacBio reads were aligned using the BLASR algorithm [50 (link)], and assembly polishing was performed with the Quiver tool (accession numbers MK861589-MK861650 and Additional file 1: Supplementary Table S2 and S3) [51 (link)].