Schistosoma haematobium

Genome Assembly & Annotation

Assembly

The S. haematobium genome presented here represents the "v2" assembly, generated using PacBio data, a long-range ("Chicago") library and Illumina sequencing. The assembly is described in full by Stroehlein et al., 2019.

Annotation

Gene models were generated using a pipeline incorporating MAKER2, EVM, and transfer from the previous "Shae.V1" gene set using liftOver and RATT. The annotation is described in full by Stroehlein et al., 2019.

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

• Stroehlein AJ, Korhonen PK, Chong TM, Lim YL, Chan KG, Webster B, Rollinson D, Brindley PJ, Gasser RB, Young ND. High-quality Schistosoma haematobium genome achieved by single-molecule and long-range sequencing. Gigascience, 2019;8(9):giz108
• Young ND, Jex AR, Li B, Liu S, Yang L, Xiong Z, Li Y, Cantacessi C, Hall RS, Xu X, Chen F, Wu X, Zerlotini A, Oliveira G, Hofmann A, Zhang G, Fang X, Kang Y, Campbell BE, Loukas A, Ranganathan S, Rollinson D, Rinaldi G, Brindley PJ, Yang H, Wang J, Wang J, Gasser RB. Whole-genome sequence of Schistosoma haematobium. Nat Genet, 2012;44(2):221-225

Navigation

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree

Gene Expression