Globodera pallida

Genome Assembly & Annotation

Assembly

Unpublished data

This is an unpublished genome project (publication pending). Before working with these data, please read our Policy for using unpublished data.

A genome assembly pipeline was used to generate a high-quality assembly from long sequencing reads. Canu was used for error correction, followed by assembly with wtdbg2. The assembly was assessed for contamination using BlobTools. A BLASTn approach was followed to further decontaminate the assembly. Contaminant contigs were removed. After finishing (FinisherSC) and purging (purge haplotigs), the assembly was subjected to long read scaffolding using SSPACE-long read v1.1 and gap filling using GapFinisher. The assembly was then polished using PacBio reads with Arrow and using both short and long reads with Pilon. The assembly was also phased using Freebayes, Whatshap, and Bcftools. All scripts used to conduct the analysis can be found here. The assembly was directly submitted to WormBase ParaSite by Dr Peter Thorpe. Awaiting publication.

Annotation

BRAKER2 was used for gene model prediction, assisted by short-read RNAseq data from Cotton et al., (2014). The resulting BRAKER predicted GFF file and the GeneMark-ET GFF files were passed to Funannotate. DIAMOND_BLASTP search against Swiss-prot was also given as evidence. The genome-guided RNAseq assembly was also passed to Funannotate, which runs PASA. The gene models were further refined in the “update” stage of Funannotate using a combination of PASA and Stringtie (Pertea et al., 2015). All scripts used to conduct the analysis can be found here. The gene models was directly submitted to WormBase ParaSite by Dr Peter Thorpe. Awaiting publication.

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

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree

Gene Expression