expam-high-resolution analysis of metagenomes using distance trees

Sean M. Solari; Remy B. Young; Vanessa R. Marcelino; Samuel C. Forster

doi:10.1093/bioinformatics/btac591

expam-high-resolution analysis of metagenomes using distance trees

Sean M. Solari, Remy B. Young, Vanessa R. Marcelino, Samuel C. Forster

Hudson Institute - Department of Molecular and Translational Science

Research output: Contribution to journal › Article › Other › peer-review

1 Citation (Scopus)

Abstract

SUMMARY: Shotgun metagenomic sequencing provides the capacity to understand microbial community structure and function at unprecedented resolution; however, the current analytical methods are constrained by a focus on taxonomic classifications that may obfuscate functional relationships. Here, we present expam, a tree-based, taxonomy agnostic tool for the identification of biologically relevant clades from shotgun metagenomic sequencing. AVAILABILITY AND IMPLEMENTATION: expam is an open-source Python application released under the GNU General Public Licence v3.0. expam installation instructions, source code and tutorials can be found at https://github.com/seansolari/expam. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Original language	English
Pages (from-to)	4814-4816
Number of pages	3
Journal	Bioinformatics
Volume	38
Issue number	20
DOIs	https://doi.org/10.1093/bioinformatics/btac591
Publication status	Published - 14 Oct 2022

Access to Document

10.1093/bioinformatics/btac591Licence: CC BY

Cite this

@article{be5f57797e3f4324bf9644d4a7642d1f,

title = "expam-high-resolution analysis of metagenomes using distance trees",

abstract = "SUMMARY: Shotgun metagenomic sequencing provides the capacity to understand microbial community structure and function at unprecedented resolution; however, the current analytical methods are constrained by a focus on taxonomic classifications that may obfuscate functional relationships. Here, we present expam, a tree-based, taxonomy agnostic tool for the identification of biologically relevant clades from shotgun metagenomic sequencing. AVAILABILITY AND IMPLEMENTATION: expam is an open-source Python application released under the GNU General Public Licence v3.0. expam installation instructions, source code and tutorials can be found at https://github.com/seansolari/expam. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.",

author = "Solari, {Sean M.} and Young, {Remy B.} and Marcelino, {Vanessa R.} and Forster, {Samuel C.}",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2022. Published by Oxford University Press.",

year = "2022",

month = oct,

day = "14",

doi = "10.1093/bioinformatics/btac591",

language = "English",

volume = "38",

pages = "4814--4816",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "20",

}

TY - JOUR

T1 - expam-high-resolution analysis of metagenomes using distance trees

AU - Solari, Sean M.

AU - Young, Remy B.

AU - Marcelino, Vanessa R.

AU - Forster, Samuel C.

N1 - Publisher Copyright: © The Author(s) 2022. Published by Oxford University Press.

PY - 2022/10/14

Y1 - 2022/10/14

N2 - SUMMARY: Shotgun metagenomic sequencing provides the capacity to understand microbial community structure and function at unprecedented resolution; however, the current analytical methods are constrained by a focus on taxonomic classifications that may obfuscate functional relationships. Here, we present expam, a tree-based, taxonomy agnostic tool for the identification of biologically relevant clades from shotgun metagenomic sequencing. AVAILABILITY AND IMPLEMENTATION: expam is an open-source Python application released under the GNU General Public Licence v3.0. expam installation instructions, source code and tutorials can be found at https://github.com/seansolari/expam. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

AB - SUMMARY: Shotgun metagenomic sequencing provides the capacity to understand microbial community structure and function at unprecedented resolution; however, the current analytical methods are constrained by a focus on taxonomic classifications that may obfuscate functional relationships. Here, we present expam, a tree-based, taxonomy agnostic tool for the identification of biologically relevant clades from shotgun metagenomic sequencing. AVAILABILITY AND IMPLEMENTATION: expam is an open-source Python application released under the GNU General Public Licence v3.0. expam installation instructions, source code and tutorials can be found at https://github.com/seansolari/expam. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

UR - http://www.scopus.com/inward/record.url?scp=85140144464&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/btac591

DO - 10.1093/bioinformatics/btac591

M3 - Article

C2 - 36029242

AN - SCOPUS:85140144464

SN - 1367-4803

VL - 38

SP - 4814

EP - 4816

JO - Bioinformatics

JF - Bioinformatics

IS - 20

ER -

expam-high-resolution analysis of metagenomes using distance trees

Abstract

Access to Document

Other files and links

Innate mucosal sensing & shaping of the human-microbiome

Phenotypic, genomic and informatic characterization of host-microbiota interactions to improve human health

Bacterial communities in metropolitan, rural and indigenous Australians

Cite this

expam-high-resolution analysis of metagenomes using distance trees

Abstract

Access to Document

Other files and links

Projects

Innate mucosal sensing & shaping of the human-microbiome

Phenotypic, genomic and informatic characterization of host-microbiota interactions to improve human health

Bacterial communities in metropolitan, rural and indigenous Australians

Cite this