bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2019-12

AUTHORS

Matthew Z. DeMaere, Aaron E. Darling

ABSTRACT

Most microbes cannot be easily cultured, and metagenomics provides a means to study them. Current techniques aim to resolve individual genomes from metagenomes, so-called metagenome-assembled genomes (MAGs). Leading approaches depend upon time series or transect studies, the efficacy of which is a function of community complexity, target abundance, and sequencing depth. We describe an unsupervised method that exploits the hierarchical nature of Hi-C interaction rates to resolve MAGs using a single time point. We validate the method and directly compare against a recently announced proprietary service, ProxiMeta. bin3C is an open-source pipeline and makes use of the Infomap clustering algorithm ( https://github.com/cerebis/bin3C ). More... »

PAGES

46

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s13059-019-1643-1

DOI

http://dx.doi.org/10.1186/s13059-019-1643-1

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1112389646

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/30808380


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Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/s13059-019-1643-1'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/s13059-019-1643-1'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/s13059-019-1643-1'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/s13059-019-1643-1'


 

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