Hymenolepis diminuta

Genome Assembly & Annotation

Assembly

Contigs were generated from paired-end and mate-pair libraries and scaffolded with long Oxford Nanopore reads using LINKS and danaasm-link, as described by Nowak et al., 2019.

Annotation

Gene models were predicted using BRAKER2 and MAKER2, guided by RNAseq data, as described by Nowak 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

• Nowak RM, Jastrzębski JP, Kuśmirek W, Sałamatin R, Rydzanicz M, Sobczyk-Kopcioł A, Sulima-Celińska A, Paukszto Ł, Makowczenko KG, Płoski R, Tkach VV, Basałaj K, Młocicki D. Hybrid de novo whole-genome assembly and annotation of the model tapeworm Hymenolepis diminuta. Sci Data, 2019;6(1):302

Navigation

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree