Amplicon library protocol for metabarcoding-based diet analysis in blue tits (Cyanistes caeruleus) using faecal DNA.This methodology uses a two-stage PCR method to produce amplicon libraries for sequencing on an Illumina MiSeq. Amplicons are required to be short (roughly 225-260 base pairs of target sequence, including priming sites) as the starting DNA, obtained from faeces, is highly degraded. Primers and PCR conditions are presented for three loci. These loci are:a.\tcytochrome oxidase subunit I (COI) - the 5\u2019 end of the Folmer region, the standard animal barcoding gene. Targets animal (in particular invertebrate) DNA.b.\t16S rRNA - a second mitochondrial gene, again targeting invertebrate DNA but also amplifying avian DNA in order to identify the species producing the faeces.c.\trbcL - a plastid gene, designed to target plant DNA.