Removal of sequencing adapter contamination improves microbial genome databases

Abstract

Abstract Advances in assembling microbial genomes have led to growth of reference genome databases, which have been transformative for applied and basic microbiome research. Here we show that published microbial genome databases from humans, mice, cows, pigs, fish, honeybees, and marine environments contain significant levels of sequencing adapter contamination that systematically reduces assembly quality. By removing the adapter-contaminated ends of contiguous sequences and reassembling, we improve the accuracy and contiguousness of genome assemblies in these databases.