Assembling Large, Complex Environmental Metagenomes

Metagenomes assembly is arguably more difficult than genome assembly, because metagenomes have characteristics of genomes (repeats) as well as transcriptomes (different subgenomes present at different levels). Titus Brown’s group posted an interesting paper at arxiv.org few weeks back, and we hope you will enjoy it. We started reading it but got scared within first paragraph, when they mentioned future goal of assembling a 20 Tb library !!

Adina Chuang Howe, Janet Jansson, Stephanie A. Malfatti, Susannah G. Tringe, James M. Tiedje, C. Titus Brown

The large volumes of sequencing data required to sample complex environments deeply pose new challenges to sequence analysis approaches. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires significant computational resources. We apply two pre- assembly filtering approaches, digital normalization and partitioning, to make large metagenome assemblies more comput\ ationaly tractable. Using a human gut mock community dataset, we demonstrate that these methods result in assemblies nearly identical to assemblies from unprocessed data. We then assemble two large soil metagenomes from matched Iowa corn and native prairie soils. The predicted functional content and phylogenetic origin of the assembled contigs indicate significant taxonomic differences despite similar function. The assembly strategies presented are generic and can be extended to any metagenome; full source code is freely available under a BSD license.

-———————–

On the topic of scalable metagenome assembler, readers may also like to read about Ray Meta covered here. C. Titus Brown, author of paper linked above, was also a reviewer of Ray Meta paper. His review opinions are posted here in his blog.