Pbjelly2

The final Illumina assembly was further scaffolded with PacBio long reads using SSPACE‐LR (LongReads) (Boetzer and Pirovano, 2014) for scaffolding, followed by GAPCloser using Illumina reads and finally gap filled with PBJelly2 (English et al., 2012) using PacBio long reads.
The assembly generated from SSPACE‐LR was gap filled with GAPCloser (Illumina Data) and PBJelly2 (PacBio long reads). PBJelly2 software is used to fill gaps in the assembly using PacBio long reads. The program is designed to handle PacBio data taking its error model into consideration. It uses a PacBio read data‐specific aligner called BLASR (Chaisson and Tesler, 2012) to map PacBio reads to the assembly and attempt to replace Ns with A, C, G or T. The final output from PBJelly2 was the first draft version of the genome.