expam—high-resolution analysis of metagenomes using distance trees

expam—high-resolution analysis of metagenomes using distance trees

SUMMARYShotgun 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 pres...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Bioinformatics (Oxford, England) England), 2022-10, Vol.38 (20), p.4814-4816
Hauptverfasser: Solari, Sean M, Young, Remy B, Marcelino, Vanessa R, Forster, Samuel C
Format: Artikel
Sprache:eng
Schlagworte:
Applications Notes
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
container_end_page 4816
container_issue 20
container_start_page 4814
container_title Bioinformatics (Oxford, England)
container_volume 38
creator Solari, Sean M
Young, Remy B
Marcelino, Vanessa R
Forster, Samuel C
description SUMMARYShotgun 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 IMPLEMENTATIONexpam 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 INFORMATIONSupplementary data are available at Bioinformatics online.
doi_str_mv 10.1093/bioinformatics/btac591
format Article
fullrecord <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_9563691</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2707611574</sourcerecordid><originalsourceid>FETCH-LOGICAL-c3061-a63edec6e143c75923dc3c6c4f3882236012214f2ea82af7de7b97158bcf23703</originalsourceid><addsrcrecordid>eNpVkctKAzEUhoMotlZfQWbpZmwuM8nMRpB6hYIbXYdM5qSNzCQ1yYjd-RA-oU9ipaXQ1fnh_HznwIfQJcHXBNds2lhvnfGhV8nqOG2S0mVNjtCYMC7yoiLkeJ8xG6GzGN8xxiUu-SkaMY5pTQs6RnfwtVL97_fP0i6WeYDouyFZ7zLlVLeONmbeZD0ktQDne4jZEK1bZK2NSTkNWQoA8RydGNVFuNjNCXp7uH-dPeXzl8fn2e081wxzkivOoAXNgRRMi7KmrNVMc10YVlWUbp4ilJLCUFAVVUa0IJpakLJqtKFMYDZBN1vuamh6aDW4FFQnV8H2KqylV1YebpxdyoX_lHXJGa_JBnC1AwT_MUBMsrdRQ9cpB36IkgosOCGlKDZVvq3q4GMMYPZnCJb_CuShArlTwP4AmWKBhA</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2707611574</pqid></control><display><type>article</type><title>expam—high-resolution analysis of metagenomes using distance trees</title><source>Oxford Journals Open Access Collection</source><source>EZB-FREE-00999 freely available EZB journals</source><source>PubMed Central</source><source>Alma/SFX Local Collection</source><creator>Solari, Sean M ; Young, Remy B ; Marcelino, Vanessa R ; Forster, Samuel C</creator><contributor>Alkan, Can</contributor><creatorcontrib>Solari, Sean M ; Young, Remy B ; Marcelino, Vanessa R ; Forster, Samuel C ; Alkan, Can</creatorcontrib><description>SUMMARYShotgun 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 IMPLEMENTATIONexpam 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 INFORMATIONSupplementary data are available at Bioinformatics online.</description><identifier>ISSN: 1367-4803</identifier><identifier>EISSN: 1367-4811</identifier><identifier>DOI: 10.1093/bioinformatics/btac591</identifier><identifier>PMID: 36029242</identifier><language>eng</language><publisher>Oxford University Press</publisher><subject>Applications Notes</subject><ispartof>Bioinformatics (Oxford, England), 2022-10, Vol.38 (20), p.4814-4816</ispartof><rights>The Author(s) 2022. Published by Oxford University Press. 2022</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c3061-a63edec6e143c75923dc3c6c4f3882236012214f2ea82af7de7b97158bcf23703</citedby><cites>FETCH-LOGICAL-c3061-a63edec6e143c75923dc3c6c4f3882236012214f2ea82af7de7b97158bcf23703</cites><orcidid>0000-0003-4144-2537</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9563691/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9563691/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,27903,27904,53769,53771</link.rule.ids></links><search><contributor>Alkan, Can</contributor><creatorcontrib>Solari, Sean M</creatorcontrib><creatorcontrib>Young, Remy B</creatorcontrib><creatorcontrib>Marcelino, Vanessa R</creatorcontrib><creatorcontrib>Forster, Samuel C</creatorcontrib><title>expam—high-resolution analysis of metagenomes using distance trees</title><title>Bioinformatics (Oxford, England)</title><description>SUMMARYShotgun 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 IMPLEMENTATIONexpam 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 INFORMATIONSupplementary data are available at Bioinformatics online.</description><subject>Applications Notes</subject><issn>1367-4803</issn><issn>1367-4811</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><recordid>eNpVkctKAzEUhoMotlZfQWbpZmwuM8nMRpB6hYIbXYdM5qSNzCQ1yYjd-RA-oU9ipaXQ1fnh_HznwIfQJcHXBNds2lhvnfGhV8nqOG2S0mVNjtCYMC7yoiLkeJ8xG6GzGN8xxiUu-SkaMY5pTQs6RnfwtVL97_fP0i6WeYDouyFZ7zLlVLeONmbeZD0ktQDne4jZEK1bZK2NSTkNWQoA8RydGNVFuNjNCXp7uH-dPeXzl8fn2e081wxzkivOoAXNgRRMi7KmrNVMc10YVlWUbp4ilJLCUFAVVUa0IJpakLJqtKFMYDZBN1vuamh6aDW4FFQnV8H2KqylV1YebpxdyoX_lHXJGa_JBnC1AwT_MUBMsrdRQ9cpB36IkgosOCGlKDZVvq3q4GMMYPZnCJb_CuShArlTwP4AmWKBhA</recordid><startdate>20221014</startdate><enddate>20221014</enddate><creator>Solari, Sean M</creator><creator>Young, Remy B</creator><creator>Marcelino, Vanessa R</creator><creator>Forster, Samuel C</creator><general>Oxford University Press</general><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0003-4144-2537</orcidid></search><sort><creationdate>20221014</creationdate><title>expam—high-resolution analysis of metagenomes using distance trees</title><author>Solari, Sean M ; Young, Remy B ; Marcelino, Vanessa R ; Forster, Samuel C</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3061-a63edec6e143c75923dc3c6c4f3882236012214f2ea82af7de7b97158bcf23703</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Applications Notes</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Solari, Sean M</creatorcontrib><creatorcontrib>Young, Remy B</creatorcontrib><creatorcontrib>Marcelino, Vanessa R</creatorcontrib><creatorcontrib>Forster, Samuel C</creatorcontrib><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Bioinformatics (Oxford, England)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Solari, Sean M</au><au>Young, Remy B</au><au>Marcelino, Vanessa R</au><au>Forster, Samuel C</au><au>Alkan, Can</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>expam—high-resolution analysis of metagenomes using distance trees</atitle><jtitle>Bioinformatics (Oxford, England)</jtitle><date>2022-10-14</date><risdate>2022</risdate><volume>38</volume><issue>20</issue><spage>4814</spage><epage>4816</epage><pages>4814-4816</pages><issn>1367-4803</issn><eissn>1367-4811</eissn><abstract>SUMMARYShotgun 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 IMPLEMENTATIONexpam 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 INFORMATIONSupplementary data are available at Bioinformatics online.</abstract><pub>Oxford University Press</pub><pmid>36029242</pmid><doi>10.1093/bioinformatics/btac591</doi><tpages>3</tpages><orcidid>https://orcid.org/0000-0003-4144-2537</orcidid><oa>free_for_read</oa></addata></record>
fulltext fulltext
identifier ISSN: 1367-4803
ispartof Bioinformatics (Oxford, England), 2022-10, Vol.38 (20), p.4814-4816
issn 1367-4803
1367-4811
language eng
recordid cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_9563691
source Oxford Journals Open Access Collection; EZB-FREE-00999 freely available EZB journals; PubMed Central; Alma/SFX Local Collection
subjects Applications Notes
title expam—high-resolution analysis of metagenomes using distance trees
url https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-24T23%3A06%3A27IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=expam%E2%80%94high-resolution%20analysis%20of%20metagenomes%20using%20distance%20trees&rft.jtitle=Bioinformatics%20(Oxford,%20England)&rft.au=Solari,%20Sean%20M&rft.date=2022-10-14&rft.volume=38&rft.issue=20&rft.spage=4814&rft.epage=4816&rft.pages=4814-4816&rft.issn=1367-4803&rft.eissn=1367-4811&rft_id=info:doi/10.1093/bioinformatics/btac591&rft_dat=%3Cproquest_pubme%3E2707611574%3C/proquest_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2707611574&rft_id=info:pmid/36029242&rfr_iscdi=true