Spherical: an iterative workflow for assembling metagenomic datasets

BMC Bioinformatics
Thomas C A Hitch, Christopher J Creevey

Abstract

The consensus emerging from the study of microbiomes is that they are far more complex than previously thought, requiring better assemblies and increasingly deeper sequencing. However, current metagenomic assembly techniques regularly fail to incorporate all, or even the majority in some cases, of the sequence information generated for many microbiomes, negating this effort. This can especially bias the information gathered and the perceived importance of the minor taxa in a microbiome. We propose a simple but effective approach, implemented in Python, to address this problem. Based on an iterative methodology, our workflow (called Spherical) carries out successive rounds of assemblies with the sequencing reads not yet utilised. This approach also allows the user to reduce the resources required for very large datasets, by assembling random subsets of the whole in a "divide and conquer" manner. We demonstrate the accuracy of Spherical using simulated data based on completely sequenced genomes and the effectiveness of the workflow at retrieving lost information for taxa in three published metagenomics studies of varying sizes. Our results show that Spherical increased the amount of reads utilized in the assembly by up to 109% co...Continue Reading

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Citations

Jul 18, 2019·FEMS Microbiology Letters·Thomas C A HitchRosalind A Gilbert
Feb 9, 2019·Frontiers in Microbiology·Javier Tamames, Fernando Puente-Sánchez
Apr 23, 2020·Frontiers in Microbiology·Ameen EetemadiIlias Tagkopoulos

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