COI Metabarcoding for fish species (Guenther et al.)

Description

Sequencing parameters:

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

Relevant publications:

• TBA

Official Methods:

• Not currently an official method.

Run with:

--primer_set COI_ILM_guenther_fish (Illumina)

--primer_set COI_IT_guenther_fish (Iontorrent)

--primer_set COI_ONT_guenther_fish (Nanopore)

For example:

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

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

Primer sequence(s)

The following primer sequences are used:

>mlCOIintF
GGWACWGGWTGAACWGTWTAYCCYCC
>jgHCO2198
TANACYTCNGGRTGNCCRAARAAYCA

Configuration

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