DNA obtained from invertebrates (iDNA) can be metabarcoded in order to survey vertebrate communities. Here, we tested for specialization by sampling the dung and carrion fly community of a swamp forest remnant along a disturbance gradient (10 sites: 80–310 m from a road). This dataset contains Illumina and MinION datasets corresponding to metabarcoding experiments on 435 fly faecal samples. This involved the amplification of 3 genes (COI 244-bp fragment, COI 313-bp fragment, and 16S) from fly faeces and regurgitates dissolved in water. Three PCR replicates were conducted for each gene and sequenced using Illumina sequencing. One replicate was then sequenced using a MinION flowcell. Flies were also independently barcoded using MinION and barcodes are included in the dataset. 

Illumina paired-end datasets corresponding to 3 PCR replicates for 3 genes: COI: 244-bp Vert-COI-flypoop-rep[1/2/3]_R[1/2]_001.fastq.gz, COI 313-bp: flypoopleray-[1/2/3]-LDJ9962_L1_[1/2].fq.gz, 16S: 16S-flypoop-rep[1/2/3]_R[1/2]_001.fastq.gz: Analysed using OBITools. 

MinION basecalled datasets corresponding to 1 PCR replicate for 3 genes: 16S: 16s_flypoop_apr22.fastq.gz, COI 244-bp: 244COI_sup.fastq.gz, COI 313-bp: lerayminion_all.fastq.gz: Using ONTbarcoder and BLAST.