Cylicocyclus nassatus

Genome Assembly & Annotation

Assembly

The full assembly process is outlined in Salle et al., (2023). HiFi data was adaptor-trimmed and filtered for low-quality reads. Genome assembly graphs were produced using HiFiasm (v0.16.1). The mitochondrial genome was assembled using the mitoHiFi v2.2 software, feeding quality filtered HiFi reads and the C. nassatus reference mitogenome as a backbone.

Annotation

The full annotation process is outlined in Salle et al., (2023). Gene annotation was conducted with the EnTAP software, to assign homology information from the EggNOG database, and protein domain information from PFAM and InterPro databases.

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

• Beier S, Fiebig A, Pommier C, Liyanage I, Lange M, Kersey PJ, Weise S, Finkers R, Koylass B, Cezard T, Courtot M, Contreras-Moreira B, Naamati G, Dyer S, Scholz U. Recommendations for the formatting of Variant Call Format (VCF) files to make plant genotyping data FAIR. F1000Res, 2022;11():ELIXIR-231

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