Lens culinaris: CDC Redberry Genome Assembly v1.2

The initial de novo sequence assembly was carried out using SOAPdenovo2 with input data consisting of 162X coverage paired end (library sizes ranging from 170-800bp) and 66X coverage mate pair data (2-8KB insert sizes). Libraries were discarded which deviated from the expected insert/fragment size. The resulting contigs were further refined using GapCloser using the initial paired end data and scaffolded with BAMBUS using a variety of large mate-pair libraries (insert sizes 20, 25, 30, 35, 40KB). PBJelly software was used for gap-filling and scaffold extension using 13X PacBio SMRT data. These scaffolds were anchored into 7 pseudomolecules using six high-density genetic linkage maps, with the total assembled bases representing over half of the 4 Gb lentil genome.