Protocol for refining metagenomic binning with BinSPreader

Sofia Ochkalova; Ivan Tolstoganov; Alla Lapidus; Anton Korobeynikov

doi:10.1016/j.xpro.2023.102417

Protocol for refining metagenomic binning with BinSPreader

STAR Protoc. 2023 Sep 15;4(3):102417. doi: 10.1016/j.xpro.2023.102417. Epub 2023 Jul 4.

Authors

Sofia Ochkalova¹, Ivan Tolstoganov², Alla Lapidus³, Anton Korobeynikov⁴

Affiliations

¹ Center for Algorithmic Biotechnology, Saint Petersburg State University, 199004 Saint Petersburg, Russia. Electronic address: so.ochkalova@gmail.com.
² Center for Algorithmic Biotechnology, Saint Petersburg State University, 199004 Saint Petersburg, Russia.
³ Center for Algorithmic Biotechnology, Saint Petersburg State University, 199004 Saint Petersburg, Russia; Department of Cytology and Histology, St. Petersburg State University, 199178 Saint Petersburg, Russia.
⁴ Center for Algorithmic Biotechnology, Saint Petersburg State University, 199004 Saint Petersburg, Russia; Department of Statistical Modelling, Saint Petersburg State University, 198504 Saint Petersburg, Russia. Electronic address: a.korobeynikov@spbu.ru.

Abstract

The analysis of metagenomic data obtained via high-throughput DNA sequencing is primarily carried out by a dedicated binning process involving clustering contigs, presumably belonging to the same species. Here, we present a protocol for improving the quality of binning using BinSPreader. We describe steps for typical metagenome assembly and binning workflow. We then detail binning refining, its variants, output, and possible caveats. This protocol optimizes the process of reconstructing more complete genomes of microorganisms that make up the metagenome. For complete details on the use and execution of this protocol, please refer to Tolstoganov et al.¹.

Keywords: Bioinformatics; Genomics; Sequence Analysis; Sequencing.

MeSH terms

Cluster Analysis
High-Throughput Nucleotide Sequencing
Metagenome* / genetics
Metagenomics* / methods
Sequence Analysis, DNA / methods