Genome Assembly Optimization Using ALLPATHS-LG

Library preparation methods were used to optimize genome assembly with the ALLPATHS-LG assembler. A 180-bp insert Illumina TruSeq fragment library was constructed from 500 ng DNA extracted from a single GSS male. This individual was the F2 offspring of an isolated mating between two GSS parents. Additionally, two Illumina Nextera mate-pair libraries targeting a 3- and 8-kb insert size, respectively, were constructed using DNA from a pool of sibling GSS males that were derived from the same isolated mating parents as the individual in the fragment library. The fragment and mate-paired libraries were sequenced using 2 × 100 bp sequencing on the Illumina HiSeq 2500 in High Output mode. The SRA accessions for each library, along with additional read counts and approximate read depths, are presented in Table 1. Raw reads from the fragment and mate pair libraries were used to construct a scaffold assembly using ALLPATHS-LG (v.44837) (Gnerre et al. 2011 (link); Ribeiro et al. 2012 (link)) with default parameters, with the exception of addition of “HAPLOIDIFY = TRUE.” Kmer-based error correction of the fragment library was performed prior to assembly as part of the ALLPATHS-LG pipeline. The draft scaffold assembly was integrated with linkage data (described in more detail in Linkage mapping and QTL analysis) and placed into chromosome-scale superscaffolds.