Assembler artifacts include misassembly because of unsafe unitigs and underassembly because of bidirected graphs.

ABSTRACT: Recent assemblies by the T2T and VGP consortia have achieved significant accuracy but required a tremendous amount of effort and resources. More typical assembly efforts, on the other hand, still suffer both from misassemblies (joining sequences that should not be adjacent) and from underassemblies (not joining sequences that should be adjacent). To better understand the common algorithm-driven causes of these limitations, we investigated the unitig algorithm, which is a core algorithm at the heart of most assemblers. We prove that, contrary to popular belief, even when there are no sequencing errors, unitigs are not always safe (i.e., they are not guaranteed to be substrings of the sequenced genome). We also prove that the unitigs of a bidirected de Bruijn graph are different from those o

SUBMITTER: Rahman A 

PROVIDER: S-EPMC9528984 | biostudies-literature | 2022 Jul

REPOSITORIES: biostudies-literature