Citing BugSeq’s methods¶

BugSeq classification algorithm¶

BugSeq’s classification algorithm is a combination of our two publications below: a hybrid read-based and assembly-based classification workflow. See the metagenomic classification page of our docs for more details

Chandrakumar I. BugSplit enables genome-resolved metagenomics through highly accurate taxonomic binning of metagenomic assemblies. Communications Biology (2022).

Fan J. BugSeq: a highly-accurate cloud platform for long-read metagenomic analysis. BMC Bioinformatics (2021).

Outbreak analysis tool¶

Khdhiri M. refMLST: reference-based multilocus sequence typing enables universal bacterial typing. BMC Bioinformatics (2024).

BugSeq’ approach to database curation¶

Chorlton SD. Ten common issues with reference sequence databases and how to mitigate them. Frontiers in Bioinformatics (2024).