title: Analysis of Illumina MiSeq Metabarcoding Data: Application to Benthic Indices for Environmental Monitoring.
abstract: This protocol details the analysis of Illumina MiSeq amplicon libraries derived from marine benthic macroinvertebrate samples and based on two barcodes of the mitochondrial cytochrome oxidase 1 (CO1) gene: a "short region," covered by overlapping forward and reverse reads and a "long region" for which forward and reverse reads do not overlap. Aside from providing guidelines for analyzing both types of amplicons, we show how amplicon reads can be used for the calculation of benthic indices for environmental monitoring.
authors.affiliation: AZTI, Marine Research Division, Txatxarramendi Ugartea z/g, E-48395, Sukarrieta, Bizkaia, Spain.
authors.forename: Eva
authors.initials: E
authors.lastname: Aylagas
authors.affiliation: AZTI, Marine Research Division, Txatxarramendi Ugartea z/g, E-48395, Sukarrieta, Bizkaia, Spain. nrodriguez@azti.es.
authors.forename: Naiara
authors.initials: N
authors.lastname: Rodríguez-Ezpeleta
mesh_terms: D000818:Animals; D044822:Biodiversity; D003576:Electron Transport Complex IV / Q000235:genetics; D004784:Environmental Monitoring / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D007448:Invertebrates / Q000145:classification / Q000235:genetics; D024101:Mitochondrial Proteins / Q000235:genetics
chemical_list: D024101:Mitochondrial Proteins; D003576:Electron Transport Complex IV
keywords: Amplicon sequencing; CO1; Folmer region; Marine benthic macroinvertebrates; MiSeq