Abstract:
BACKGROUND:A metagenomic sample is a set of DNA fragments, randomly extracted from multiple cells in an environment, belonging to distinct, often unknown species. Unsupervised metagenomic clustering aims at partitioning a metagenomic sample into sets that approximate taxonomic units, without using reference genomes. Since samples are large and steadily growing, space-efficient clustering algorithms are strongly needed. RESULTS:We design and implement a space-efficient algorithmic framework that solves a number of core primitives in unsupervised metagenomic clustering using just the bidirectional Burrows-Wheeler index and a union-find data structure on the set of reads. When run on a sample of total length n, with m reads of maximum length ℓ each, on an alphabet of total size σ, our algorithms take O(n(t+logσ)) time and just 2n+o(n)+O(max{ℓ σlogn,K logm}) bits of space in addition to the index and to the union-find data structure, where K is a measure of the redundancy of the sample and t is the query time of the union-find data structure. CONCLUSIONS:Our experimental results show that our algorithms are practical, they can exploit multiple cores by a parallel traversal of the suffix-link tree, and they are competitive both in space and in time with the state of the art.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Alanko J,Cunial F,Belazzougui D,Mäkinen Vdoi
10.1186/s12859-017-1466-6subject
Has Abstractpub_date
2017-03-14 00:00:00pages
59issue
Suppl 3issn
1471-2105pii
10.1186/s12859-017-1466-6journal_volume
18pub_type
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