Trycycler: consensus long-read assemblies for bacterial genomes

Genome Biol. 2021 Sep 14;22(1):266. 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.

Keywords: Bacterial genomics; Genome assembly; Long-read sequencing; Oxford Nanopore sequencing; Whole-genome sequencing.

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Consensus Sequence
  • Genome, Bacterial*
  • High-Throughput Nucleotide Sequencing / methods*
  • Sequence Analysis, DNA / methods*
  • Software*