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A Scalable Reference-Free Metagenomic Binning Pipeline

  • Terry Ma
  • Xin Xing
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10847)

Abstract

Metagenomics studies microbial genomes in an ecosystem such as the gastrointestinal tract of a human through sequencing thousands of organism in parallel. The sheer number of genomic fragments are challenging for current metagenomic binning software to process. Here we present a scalable reference-free metagenomic binning pipeline designed to handle large scale metagenomic data. It allows users to input several tera base pairs (TB) of reads and produces highly accurate binning results, even at a species level. The pipeline outputs all binned species in multiple metagenomic samples and their estimated relative abundance. We integrate the pipeline into an open-source software, MetaMat, which is freely available at: https://github.com/BioAlgs/MetaMat.

Keywords

Metagenomic binning Parallel computing Disease diagnosis 

Notes

Acknowledgement

This research was supported in part by the National Institutes of Health grant R01 GM113242-01 and the National Science Foundation grants DMS-1440038 and DMS-1440037.

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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Lambert High SchoolSuwaneeUSA
  2. 2.University of GeorgiaAthensUSA

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