Paper draft: Scaling metagenome sequence assembly with probabilistic de Bruijn graphs

(updated to point to http://arxiv.org/).

Authors: Jason Pell, Arend Hintze, Rosangela Canino-Koning, Adina Howe, James M. Tiedje, C. Titus Brown

Abstract:

The memory requirements for de novo assembly of short-read shotgun sequencing data from complex microbial populations are an increasingly large practical barrier to environmental studies. Here we introduce a memory-efficient graph representation with which we can analyze the k-mer connectivity of metagenomic samples, allowing us to reduce the size of the de novo assembly process for metagenomes with a "divide and conquer" algorithm. This graph representation is based on a probabilistic data structure, a Bloom filter, that allows us to store assembly graphs in as little as 4 bits per k-mer. We use this approach to achieve a 20-fold decrease in memory for the assembly of a soil metagenome sample.

The paper is available on arXiv here: http://arxiv.org/abs/1112.4193. Comments are welcome! We're planning to submit it to PNAS later this week.

I'll write a longer blog post about it soon.

--titus

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