Oncorhynchus tshawytscha isolate:JC-2011-M1 Genome sequencing and assembly

The genome was sequenced with a combination of TruSeq long-read libraries, BAC libraries, mate-pair libraries (3-40kb) and BioNano optical maps. TruSeq and BAC libraries were assembled with SPADES to obtain synthetic long reads, followed by a whole genome assembly using CELERA. Resulting contigs were scaffolded using mate-pairs libraries with FAST-SG+OPERA-LG. Scaffolds were error-corrected using optical maps with BioNano Access v.1.0. Finally, scaffolds were ordered into chromosomes with available genetic maps (Brieuc et al. 2014; McKinney et al. 2015) and whole genome alignments to a reference rainbow trout genome (Palti et al. 2017). The resulting assembly has a total size of 2.36Gb with a contig N50 of 19.1Kb, scaffold N50 of 153Kb and 72% (1.7Gb) of the assembly anchored to chromosomes (N50 45.4Mb).