Genome Assembly & Annotation
The draft genome assembly was produced by the Parasite Genomic group at the Wellcome Trust Sanger Institute, in collaboration with Adrian Streit (Max Planck Institute for Developmental Biology), using Illumina paired-end sequencing followed by an in-house genome assembly pipeline comprising various steps, including contig assembly, scaffolding, gap-filling and error-correction, followed by some bespoke manual improvement, including the use of genetic markers described by Nemetschke et al, 2010 (WTSI Strongyloididae Nematode Genomes Project, Hunt et al. (2016)).
The gene predictions were made by the Parasite Genomics group at the Wellcome Trust Sanger Institute as part of the Strongyloididae Nematode Genomes Project, Hunt et al. (2016). An in-house automatic pipeline (based around AUGUSTUS plus MAKER) was used to generate first-pass gene models, and this was followed by a round of targeted manual curation of selected gene families.
- Nemetschke L, Eberhardt AG, Hertzberg H, Streit A. Genetics, chromatin diminution, and sex chromosome evolution in the parasitic nematode genus Strongyloides. Curr Biol, 2010;20(19):1687-1696
- Hunt VL, Tsai IJ, Coghlan A, Reid AJ, Holroyd N, Foth BJ, Tracey A, Cotton JA, Stanley EJ, Beasley H, Bennett HM, Brooks K, Harsha B, Kajitani R, Kulkarni A, Harbecke D, Nagayasu E, Nichol S, Ogura Y, Quail MA, Randle N, Xia D, Brattig NW, Soblik H, Ribeiro DM, Sanchez-Flores A, Hayashi T, Itoh T, Denver DR, Grant W, Stoltzfus JD, Lok JB, Murayama H, Wastling J, Streit A, Kikuchi T, Viney M, Berriman M. The genomic basis of parasitism in the Strongyloides clade of nematodes. Nat Genet, 2016;48(3):299-307
|Data Source||Wellcome Trust Sanger Institute|
This widget has been derived from the assembly-stats code developed by the Lepbase project at the University of Edinburgh