Lightweight taxonomic profiling of long-read sequenced metagenomes with Lemur and Magnet

Sapoval, N.; Liu, Y.; Curry, K.; Kille, B.; Huang, W.; Kokroko, N.; Nute, M. G.; Tyshaieva, A.; Dilthey, A. T.; Molloy, E.; Treangen, T. J.

doi:10.1101/2024.06.01.596961

bioRxiv · 10.1101/2024.06.01.596961

Lightweight taxonomic profiling of long-read sequenced metagenomes with Lemur and Magnet

Sapoval, N.·Liu, Y.·Curry, K.·Kille, B.·Huang, W.·Kokroko, N.·Nute, M. G.·Tyshaieva, A.·Dilthey, A. T.·Molloy, E.·Treangen, T. J.

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Abstract

The advent of long-read sequencing of microbiomes necessitates the development of new taxonomic profilers tailored to long-read shotgun metagenomic datasets. Here, we introduce Lemur and Magnet, a pair of tools optimized for lightweight and accurate taxonomic profiling for long-read shotgun metagenomic datasets. Lemur is a marker-gene-based method that leverages an EM algorithm to reduce false positive calls while preserving true positives; Magnet is a whole-genome read-mapping-based method that provides detailed presence and absence calls for bacterial genomes. We demonstrate that Lemur and Magnet can run in minutes to hours on a laptop with 32 GB of RAM, even for large inputs, a crucial feature given the portability of long-read sequencing machines. Furthermore, the marker gene database used by Lemur is only 4 GB and contains information from over 300,000 RefSeq genomes. Lemur and Magnet are open-source and available at https://github.com/treangenlab/lemur and https://github.com/treangenlab/magnet.

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Sapoval, N., Liu, Y., Curry, K., Kille, B., Huang, W., Kokroko, N., Nute, M. G., Tyshaieva, A., Dilthey, A. T., Molloy, E., Treangen, T. J.. 2024-06-03. Lightweight taxonomic profiling of long-read sequenced metagenomes with Lemur and Magnet. https://doi.org/10.1101/2024.06.01.596961

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