Strongyloides ratti

Genome Assembly & Annotation

Assembly

The reference genome was assembled by the Parasite Genomic group at the Wellcome Trust Sanger Institute, in collaboration with Mark Viney (University of Bristol), using a combination of capillary, 454 and Illumina paired-end sequence and genetic map data, and improved using bespoke manual and automated tools (WTSI Strongyloididae Nematode Genomes Project, Hunt et al. (2016)).

Annotation

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.

Downloads

• Genomic Sequence (FASTA)
• Hard-masked Genomic Sequence (FASTA)
• Soft-masked Genomic Sequence (FASTA)
• Annotations (GFF3)
• Proteins (FASTA)
• Full-length transcripts (FASTA)
• CDS transcripts (FASTA)

Tools

• Search for sequences in the genome and proteome using BLAST
• Work with lists of data using the WormBase ParaSite BioMart data-mining tool
• Programatically access WormBase ParaSite data using the REST API
• Predict the effects of variants using the Variant Effect Predictor

Key Publications

• Nemetschke L, Eberhardt AG, Viney ME, Streit A. A genetic map of the animal-parasitic nematode Strongyloides ratti. Mol Biochem Parasitol, 2010;169(2):124-127
• 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

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