Schistosoma spindale

Genome Assembly & Annotation

Assembly

This annotated genome assembly was produced as part of the doctoral thesis of Duncan Berger: [Berger, D. (2021). Comparative and population genomic analyses of the parasitic blood flukes (Doctoral thesis)](https://doi.org/10.17863/CAM.86667).

The assembly was generated from PacBio long-read sequencing data and scaffolded using Hi-C.

The source material for genome sequencing was two adult male worms, originally obtained from Sri Lanka in 2007, archived as part of the SCAN collection at the Natural History Museum, London, and provided by Fiona Allan, Aidan Emery and Muriel Rabone. Additional worms from the same collection were used for gene finding.

Annotation

Gene finding employed a customized pipeline that integrated RNA-Seq, Iso-Seq and homology data. Berger, D. (2021). Comparative and population genomic analyses of the parasitic blood flukes (Doctoral thesis).

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

Navigation

View karyotype

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree