Trycycler: consensus long-read assemblies for bacterial genomes

• Published in: Genome Biology Vol. 22; no. 1; p. 266
• Main Authors: Wick, Ryan R, Judd, Louise M, Cerdeira, Louise T, Hawkey, Jane, Méric, Guillaume, Vezina, Ben, Wyres, Kelly L, Holt, Kathryn E
• Format: Journal Article
• Language: English
• Published: England BioMed Central 14-09-2021; BMC
• Subjects: Bacterial genomics; Consensus Sequence; Genome assembly; Genome, Bacterial; Genomes; High-Throughput Nucleotide Sequencing - methods; Long-read sequencing; Oxford Nanopore sequencing; Plasmids; Reconciliation; Sequence Analysis, DNA - methods; Software; Whole-genome sequencing; Long-read sequencing; Genome assembly; Bacterial genomics; Whole-genome sequencing; Oxford Nanopore sequencing
• ISSN: 1474-760X; 1474-7596; 1474-760X
• DOI: 10.1186/s13059-021-02483-z

While long-read sequencing allows for the complete assembly of bacterial genomes, long-read assemblies contain a variety of errors. Here, we present Trycycler, a tool which produces a consensus assembly from multiple input assemblies of the same genome. Benchmarking showed that Trycycler assemblies contained fewer errors than assemblies constructed with a single tool. Post-assembly polishing further reduced errors and Trycycler+polishing assemblies were the most accurate genomes in our study. As Trycycler requires manual intervention, its output is not deterministic. However, we demonstrated that multiple users converge on similar assemblies that are consistently more accurate than those produced by automated assembly tools.