Prevalence and Implications of Contamination in Public Genomic Resources: A Case Study of 43 Reference Arthropod Assemblies.

ABSTRACT: Thanks to huge advances in sequencing technologies, genomic resources are increasingly being generated and shared by the scientific community. The quality of such public resources are therefore of critical importance. Errors due to contamination are particularly worrying; they are widespread, propagate across databases, and can compromise downstream analyses, especially the detection of horizontally-transferred sequences. However we still lack consistent and comprehensive assessments of contamination prevalence in public genomic data. Here we applied a standardized procedure for foreign sequence annotation to 43 published arthropod genomes from the widely used Ensembl Metazoa database. This method combines information on sequence similarity and synteny to identify contaminant and putative

SUBMITTER: Francois CM 

PROVIDER: S-EPMC7003083 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature