Network analysis with either Illumina or MinION reveals that detecting vertebrate species requires metabarcoding of iDNA from a diverse fly community

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.