Halicephalobus sp. NKZ332

Genome Assembly & Annotation

Assembly

The draft genome assembly was produced by the [Department of Biology at the Indiana University](http://www.sanger.ac.uk/research/projects/parasitegenomics/. The assembly uses Illumina NextSeq 300bp paired-end sequencing. Minia and SPAdes assemblers were used to perform a de-contaminated assembly.

Annotation

The gene predictions were made by the [Department of Biology at the Indiana University](http://www.sanger.ac.uk/research/projects/parasitegenomics/. An in-house pipeline was developed that used MAKER to generate high-quality annotations by integrating evidence from multiple sources: protein sequences from UniProt, the hidden Markov model (HMM) computed from GeneMark and the BUSCO generated AUGUSTUS profile. Predicted genes from the MAKER output were used to train and run AUGUSTUS to produce the final annotation.

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

• Ragsdale EJ, Koutsovoulos G, Biddle JF. A draft genome for a species of <i>Halicephalobus</i> (Panagrolaimidae). J Nematol, 2019;51():1-4

Navigation

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree