Assessing the de novo assemblers: a metaviromic study of apple and first report of citrus concave gum-associated virus, apple rubbery wood virus 1 and 2 infecting apple in India.

ABSTRACT:

Background

The choice of de novo assembler for high-throughput sequencing (HTS) data remains a pivotal factor in the HTS-based discovery of viral pathogens. This study assessed de novo assemblers, namely Trinity, SPAdes, and MEGAHIT for HTS datasets generated on the Illumina platform from 23 apple samples, representing 15 exotic and indigenous apple varieties and a rootstock. The assemblers were compared based on assembly quality metrics, including the largest contig, total assembly length, genome coverage, and N50.

Results

MEGAHIT was most efficient assembler according to the metrics evaluated in this study. By using multiple assemblers, near-complete genome sequences of citrus concave gum-associated virus (CCGaV), apple rubbery wood virus 1 (ARWV-1), ARWV-2, apple necrotic

SUBMITTER: Khan ZA 

PROVIDER: S-EPMC11546112 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature