Article

StrainPanDA: linked reconstruction of strain composition and gene content profiles via pangenome-based decomposition of metagenomic data

2022-02-19

Abstract excerpt

<h4>Background</h4> Microbial strains of variable functional capacities co-exist in microbiomes. Current bioinformatics methods of strain analysis cannot provide the direct linkage between strain composition and their gene contents from metagenomic data. <h4>Methods</h4> Here we present StrainPanDA ( Strain -level Pan genome D ecomposition A nalysis), a novel method that uses the pangenome coverage profile o...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: 1b424655-735a-5dd2-8489-f9c24349dad0
DOI: 10.1101/2022.02.15.480535

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

StrainPanDA: linked reconstruction of strain composition and gene content profiles via pangenome-based decomposition of metagenomic dataDOI 10.1101/2022.02.15.480535Read

Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGCSemantic proximity Read

Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC.Semantic proximity Read

Quantifying Metagenomic Strain Associations from Microbiomes with AnpanSemantic proximity Read

An evolution-based framework for describing human gut bacteriaSemantic proximity Read

Strain profiling and epidemiology of bacterial species from metagenomic sequencing.Semantic proximity Read

An integrated strain-level analytic pipeline utilizing longitudinal metagenomic data.Semantic proximity Read

MAGinator enables strain-level quantification of <i>de novo</i> MAGsSemantic proximity Read

Accurate profiling of microbial communities for shotgun metagenomic sequencing with Meteor2Semantic proximity Read

StrainXpress: strain aware metagenome assembly from short readsSemantic proximity Read

StrainGE: A toolkit to track and characterize low-abundance strains in complex microbial communitiesSemantic proximity Read

StrainXpress: strain aware metagenome assembly from short readsSemantic proximity Read

Benchmarking strain-level profiling of <i>Escherichia coli</i> in short-read gut metagenomesSemantic proximity Read