Trileptium ribeirensis

Genome Assembly & Annotation

Assembly

The full assembly process is described in Lee et al., (2023). The Flye assembler (ver. 2.9.1) was used to assemble the raw ONT reads. These were then polished by four iterations of Racon (ver. 1.4.11), followed by Medaka (ver. 1.2.0; option: -m r941_min_sup_g507 or r103_sup_g507). The consensus sequences were further corrected with Illumina reads using NextPolish(ver. 1.4.0), and haplotigs were removed using HaploMerger2 (ver. 20180603). Assemblies were mapped to the reference genome with minimap2 (option: -ax asm5). Raw Illumina reads were assembled using the Spades assembler (ver. v3.14.1; option: spades_sc).

Annotation

The full annotation process is described in Lee et al., (2023). Single-worm transcriptome reads were mapped to the corresponding genome assemblies using STAR (ver. 2.7.7a). The gene models were predicted using BRAKER2 (ver. 2.1.6; option: –etpmode) with proteomes and RNA-seq mappings as evidence hints. Transcript predictions were mapped to the reference genome using Minimap2 (-ax splice), converted to gff format and compared against the reference proteome using Gffcompare (ver. v0.11.2).

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

• Lee YC, Ke HM, Liu YC, Lee HH, Wang MC, Tseng YC, Kikuchi T, Tsai IJ. Single-worm long-read sequencing reveals genome diversity in free-living nematodes. Nucleic Acids Res, 2023;51(15):8035-8047

Navigation

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree