AFS : identification and quantification of species composition by metagenomic sequencing
© The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissionsoup.com.
Summary: DNA-based methods to detect and quantify taxon composition in biological materials are often based on species-specific polymerase chain reaction, limited to detecting species targeted by the assay. Next-generation sequencing overcomes this drawback by untargeted shotgun sequencing of whole metagenomes at affordable cost. Here we present AFS, a software pipeline for quantification of species composition in food. AFS uses metagenomic shotgun sequencing and sequence read counting to infer species proportions. Using Illumina data from a reference sausage comprising four species, we reveal that AFS is independent of the sequencing assay and library preparation protocol. Cost-saving short (50-bp) single-end reads and Nextera ® library preparation yield reliable results.
Availability and Implementation: Datasets, binaries and usage instructions are available under http://all-food-seq.sourceforge.net. Raw data is available at NCBI's SRA with accession number PRJNA271645.
Contact: hankelnuni-mainz.de.
Supplementary information: Supplementary data are available at Bioinformatics online.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2017 |
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| Erschienen: |
2017 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:33 |
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| Enthalten in: |
Bioinformatics (Oxford, England) - 33(2017), 9 vom: 01. Mai, Seite 1396-1398 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Liu, Yongchao [VerfasserIn] |
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| Anmerkungen: |
Date Completed 30.01.2018 Date Revised 18.03.2022 published: Print Citation Status MEDLINE |
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| doi: |
10.1093/bioinformatics/btw822 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| PPN (Katalog-ID): |
NLM271395982 |
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| 500 | |a Date Revised 18.03.2022 | ||
| 500 | |a published: Print | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissionsoup.com | ||
| 520 | |a Summary: DNA-based methods to detect and quantify taxon composition in biological materials are often based on species-specific polymerase chain reaction, limited to detecting species targeted by the assay. Next-generation sequencing overcomes this drawback by untargeted shotgun sequencing of whole metagenomes at affordable cost. Here we present AFS, a software pipeline for quantification of species composition in food. AFS uses metagenomic shotgun sequencing and sequence read counting to infer species proportions. Using Illumina data from a reference sausage comprising four species, we reveal that AFS is independent of the sequencing assay and library preparation protocol. Cost-saving short (50-bp) single-end reads and Nextera ® library preparation yield reliable results | ||
| 520 | |a Availability and Implementation: Datasets, binaries and usage instructions are available under http://all-food-seq.sourceforge.net. Raw data is available at NCBI's SRA with accession number PRJNA271645 | ||
| 520 | |a Contact: hankelnuni-mainz.de | ||
| 520 | |a Supplementary information: Supplementary data are available at Bioinformatics online | ||
| 650 | 4 | |a Journal Article | |
| 700 | 1 | |a Ripp, Fabian |e verfasserin |4 aut | |
| 700 | 1 | |a Koeppel, Rene |e verfasserin |4 aut | |
| 700 | 1 | |a Schmidt, Hanno |e verfasserin |4 aut | |
| 700 | 1 | |a Hellmann, Sören Lukas |e verfasserin |4 aut | |
| 700 | 1 | |a Weber, Mathias |e verfasserin |4 aut | |
| 700 | 1 | |a Krombholz, Christopher Felix |e verfasserin |4 aut | |
| 700 | 1 | |a Schmidt, Bertil |e verfasserin |4 aut | |
| 700 | 1 | |a Hankeln, Thomas |e verfasserin |4 aut | |
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