Hybracter: enabling scalable, automated, complete and accurate bacterial genome assemblies

George Bouras, Ghais Houtak, Ryan R. Wick, Vijini Mallawaarachchi, Michael J. Roach, Bhavya Papudeshi, Lousie M. Judd, Anna E. Sheppard, Robert A. Edwards, Sarah Vreugde

Research output: Contribution to journalArticlepeer-review

4 Citations (Scopus)
52 Downloads (Pure)

Abstract

Improvements in the accuracy and availability of long-read sequencing mean that complete bacterial genomes are now routinely reconstructed using hybrid (i.e. short- and long-reads) assembly approaches. Complete genomes allow a deeper understanding of bacterial evolution and genomic variation beyond single nucleotide variants. They are also crucial for identifying plasmids, which often carry medically significant antimicrobial resistance genes. However, small plasmids are often missed or misassembled by long-read assembly algorithms. Here, we present Hybracter which allows for the fast, automatic and scalable recovery of near-perfect complete bacterial genomes using a long-read first assembly approach. Hybracter can be run either as a hybrid assembler or as a long-read only assembler. We compared Hybracter to existing automated hybrid and long-read only assembly tools using a diverse panel of samples of varying levels of long-read accuracy with manually curated ground truth reference genomes. We demonstrate that Hybracter as a hybrid assembler is more accurate and faster than the existing gold standard automated hybrid assembler Unicycler. We also show that Hybracter with long-reads only is the most accurate long-read only assembler and is comparable to hybrid methods in accurately recovering small plasmids.
Original languageEnglish
Article number001244
Number of pages15
JournalMicrobial Genomics
Volume10
Issue number5
DOIs
Publication statusPublished - May 2024

Keywords

  • Long-reads
  • Assembly
  • Plasmids
  • long-reads
  • assembly
  • plasmids

Fingerprint

Dive into the research topics of 'Hybracter: enabling scalable, automated, complete and accurate bacterial genome assemblies'. Together they form a unique fingerprint.

Cite this