COI Metabarcoding for insect species (Park et al.)

Description

Sequencing parameters:

• Platform: Illumina, IonTorrent and Nanopore
• Read-length: paired-end 250bp or longer, single-end with 450bp or longer
• Targets: insects

Relevant publications:

• Barcoding Bugs: DNA-Based Identification of the True Bugs (Insecta: Hemiptera: Heteroptera)
• Molecular systematics of cowries (Gastropoda: Cypraeidae) and diversification patterns in the tropics

Official Methods:

• Not currently an official method.

Run with:

--primer_set COI_ILM_park_insects (Illumina)

--primer_set COI_IT_park_insects (Iontorrent)

--primer_set COI_ONT_park_insects (Nanopore)

For example:

nextflow run bio-raum/FooDMe2 \
  -r main \
  -profile myprofile \ # (1)!
  --input samples.tsv \
  --primer_set COI_ILM_park_insects

1. See the installation guide for more details on this parameter

Primer sequence(s)

The following primer sequences are used:

>Fwd-Insekten-COI
GCATTYCCACGAATAAATAAYATAAG
>Rev-Insekten-COI
TAAACTTCAGGGTGACCAAARAAYCA

Configuration

Check the relevant configuration file under conf/primers/ for an list of parameters (e.g. COI_ILM_park_insects.conf).