In:
Bioinformatics, Oxford University Press (OUP), Vol. 33, No. 9 ( 2017-05-01), p. 1396-1398
Abstract:
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. Supplementary information Supplementary data are available at Bioinformatics online.
Type of Medium:
Online Resource
ISSN:
1367-4803
,
1367-4811
DOI:
10.1093/bioinformatics/btw822
Language:
English
Publisher:
Oxford University Press (OUP)
Publication Date:
2017
detail.hit.zdb_id:
1468345-3
SSG:
12