Article Dans Une Revue Nucleic Acids Research Année : 2024

Annotation and visualization of parasite, fungi and arthropod genomes with Companion

Résumé

As sequencing genomes has become increasingly popular, the need for annotation of the resulting assemblies is growing. Structural and functional annotation is still challenging as it includes finding the correct gene sequences, annotating other elements such as RNA and being able to submit those data to databases to share it with the community. Compared to de novo assembly where contiguous chromosomes are a sign of high quality, it is difficult to visualize and assess the quality of annotation. We developed the Companion web server to allow non-experts to annotate their genome using a reference-based method, enabling them to assess the output before submitting to public databases. In this update paper, we describe how we have included novel methods for gene finding and made the Companion server more efficient for annotation of genomes of up to 1 Gb in size. The reference set was increased to include genomes of interest for human and animal health from the fungi and arthropod kingdoms. We show that Companion outperforms existing comparable tools where closely related references are available.

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Domaines

Immunologie

Dates et versions

hal-04753935 , version 1 (25-10-2024)

Identifiants

Citer

William Haese-Hill, Kathryn Crouch, Thomas Otto. Annotation and visualization of parasite, fungi and arthropod genomes with Companion. Nucleic Acids Research, 2024, 52 (W1), pp.W39-W44. ⟨10.1093/nar/gkae378⟩. ⟨hal-04753935⟩
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