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Göteborgs universitets publikationer

Metaxa2 Diversity Tools: Easing microbial community analysis with Metaxa2

Författare och institution:
Johan Bengtsson-Palme (Institutionen för biomedicin, avdelningen för infektionssjukdomar); Kaisa Thorell (-); Christian Wurzbacher (Institutionen för biologi och miljövetenskap); Åsa Sjöling (-); R. Henrik Nilsson (Institutionen för biologi och miljövetenskap)
Publicerad i:
Ecological Informatics, 33 s. 45-50
ISSN:
1574-9541
Publikationstyp:
Artikel, refereegranskad vetenskaplig
Publiceringsår:
2016
Språk:
engelska
Fulltextlänk:
Sammanfattning (abstract):
DNA sequencing has become an integrated part of microbial ecology, and taxonomic marker genes such as the SSU and LSU rRNA are frequently used to assess community structure. One solution for taxonomic community analysis based on shotgun metagenomic data is the Metaxa2 software, which can extract and classify sequence fragments belonging to the rRNA genes. This paper describes the Metaxa2 Diversity Tools, a set of new open-source software programs that extends the capabilities of the Metaxa2 software. These tools allow for better handling of data from multiple samples, improved species classifications, rarefaction analysis accounting for unclassified entries, and determination of significant differences in community composition of different samples. We demonstrate the performance of the software tools on rRNA data extracted from different shotgun metagenomes, and find the tools to streamline and improve the assessments of community diversity, particularly for samples from environments for which few reference genomes are available. Finally, we establish that our resampling algorithm for determining community dissimilarity is robust to differences in coverage depth, suggesting that it forms a complement to multidimensional visualization approaches for finding differences between communities. The Metaxa2 Diversity Tools are included in recent versions (2.1 and later) of Metaxa2 (http://microbiology.se/software/metaxa2/) and facilitate implementation of Metaxa2 within software pipelines for taxonomic analysis of environmental communities.
Ämne (baseras på Högskoleverkets indelning av forskningsämnen):
NATURVETENSKAP ->
Biologiska vetenskaper ->
Mikrobiologi
NATURVETENSKAP ->
Biologiska vetenskaper ->
Bioinformatik och systembiologi
NATURVETENSKAP ->
Biologiska vetenskaper ->
Ekologi
Nyckelord:
Community similarity, Diversity assessment, Metagenomics, Microbial communities, rRNA, Rarefaction analysis
Postens nummer:
236688
Posten skapad:
2016-05-18 14:43
Posten ändrad:
2016-05-31 14:49

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