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Spherical: an iterative workflow for assembling metagenomic datasets

Thomas Hitch, Christopher J Creevey
doi: https://doi.org/10.1101/067256
Thomas Hitch
1Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, SY23 3FG, UK
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Christopher J Creevey
1Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, SY23 3FG, UK
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Abstract

The consensus emerging from microbiome studies is that they are far more complex than previously thought, requiring deep sequencing. As deep sequenced datasets provide greater coverage than previous datasets, recovering a higher proportion of reads to the assembly is still a challenge. To tackle this issue, we set of to identify if multiple iterations of assembly would allow for otherwise lost contigs to be formed and studied and if so, how successful is such an avenue at improving the current methodology.

A simulated metagenomic dataset was initially used to identify if multiple iterations of assembly produce useable contigs or mis-assembled artefacts were produced. Once we had confirmed that the secondary iterations were producing both accurate contigs without a reduction in contig quality we applied this methodology in the form of Spherical to 3 metagenomic studies.

The additional contigs produced by Spherical increased the number of reads aligning to an identified gene by 11–109% compared to the initial iterations assembly. As the size of the dataset increased, as did the amount of data multiple iterations were able to add.

Availability Spherical is implemented in Python 2.7 and available for use under a MIT licence agreement at: https://github.com/thh32/Spherical

Footnotes

  • Contact information: Chris Creevey, chc30{at}aber.ac.uk

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted August 02, 2016.
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Spherical: an iterative workflow for assembling metagenomic datasets
Thomas Hitch, Christopher J Creevey
bioRxiv 067256; doi: https://doi.org/10.1101/067256
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Spherical: an iterative workflow for assembling metagenomic datasets
Thomas Hitch, Christopher J Creevey
bioRxiv 067256; doi: https://doi.org/10.1101/067256

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