Monitoring of four DNA extraction methods upstream of high-throughput sequencing of Anisakidae nematodes

Different methods were evaluated to extract DNA from pooled nematodes belonging to Anisakis, Contracaecum, Pseudoterranova and Hysterothylacium genera isolated from edible fish. Pooled DNA extraction is the first and compulsory step to allow the identification of a large number of samples through high-throughput DNA sequencing with drastic time and cost reductions. •We evaluated 4 methods of DNA extraction from Anisakid nematodes.•The DNA extraction protocols were adapted to high quantities of nematodes.•We monitored for DNA quality/quantity and for the presence of inhibitors by qPCR.•The anion-exchange resin method gave the best purification and yield of nematode DNA.•The DNA can be subsequently used for downstream high-throughput sequencing of COX2.