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Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding
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SYSNO ASEP 0498742 Druh ASEP J - Článek v odborném periodiku Zařazení RIV J - Článek v odborném periodiku Poddruh J Článek ve WOS Název Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding Tvůrce(i) Aslan, S. (DE)
Nilsson, R.H. (SE)
Wurzbacher, Ch. (DE)
Baldrian, Petr (MBU-M) RID, ORCID
Tedersoo, L. (EE)
Bahram, M. (EE)Zdroj.dok. MycoKeys. - : Pensoft Publishers - ISSN 1314-4057
Roč. 39, SEP 10 (2018), s. 29-40Poč.str. 12 s. Jazyk dok. eng - angličtina Země vyd. BG - Bulharsko Klíč. slova Microbial communities ; microbiome ; fungal biodiversity Vědní obor RIV EE - Mikrobiologie, virologie Obor OECD Microbiology Institucionální podpora MBU-M - RVO:61388971 UT WOS 000444106400001 EID SCOPUS 85054060226 DOI 10.3897/mycokeys.39.28109 Anotace Along with recent developments in high-throughput sequencing (HTS) technologies and thus fast accumulation of HTS data, there has been a growing need and interest for developing tools for HTS data processing and communication. In particular, a number of bioinformatics tools have been designed for analysing metabarcoding data, each with specific features, assumptions and outputs. To evaluate the potential effect of the application of different bioinformatics workflow on the results, we compared the performance of different analysis platforms on two contrasting high-throughput sequencing data sets. Our analysis revealed that the computation time, quality of error filtering and hence output of specific bioinformatics process largely depends on the platform used. Our results show that none of the bioinformatics workflows appears to perfectly filter out the accumulated errors and generate Operational Taxonomic Units, although PipeCraft, LotuS and PIPITS perform better than QIIME2 and Galaxy for the tested fungal amplicon dataset. We conclude that the output of each platform requires manual validation of the OTUs by examining the taxonomy assignment values. Pracoviště Mikrobiologický ústav Kontakt Eliška Spurná, eliska.spurna@biomed.cas.cz, Tel.: 241 062 231 Rok sběru 2019
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