Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388971%3A_____%2F18%3A00498742" target="_blank" >RIV/61388971:_____/18:00498742 - isvavai.cz</a>
Result on the web
<a href="http://dx.doi.org/10.3897/mycokeys.39.28109" target="_blank" >http://dx.doi.org/10.3897/mycokeys.39.28109</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.3897/mycokeys.39.28109" target="_blank" >10.3897/mycokeys.39.28109</a>
Alternative languages
Result language
angličtina
Original language name
Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding
Original language description
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.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10606 - Microbiology
Result continuities
Project
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Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2018
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
MycoKeys
ISSN
1314-4057
e-ISSN
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Volume of the periodical
39
Issue of the periodical within the volume
SEP 10
Country of publishing house
BG - BULGARIA
Number of pages
12
Pages from-to
29-40
UT code for WoS article
000444106400001
EID of the result in the Scopus database
2-s2.0-85054060226