Welcome to SPARSE’s documentation!

SPARSE indexes >100,000 reference genomes in public databases into hierarchical clusters and uses it to predict origins of metagenomic reads.


SPARSE has been pulished as a conference paper in RECOMB 2018. Zhou Z., Luhmann N., Alikhan NF., Quince C., Achtman M. (2018) Accurate Reconstruction of Microbial Strains from Metagenomic Sequencing Using Representative Reference Genomes. In: Raphael B. (eds) Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science, vol 10812. Springer, Cham. DOI: https://doi.org/10.1007/978-3-319-89929-9_15

A preprint can also be found in BioRxiv : https://www.biorxiv.org/content/early/2017/11/07/215707

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