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alexpiper / taxreturn

An R package for creating taxonomic reference databases for metabarcoding studies
GNU General Public License v3.0
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Retrieving COI from mitogenome #10

Closed alexpiper closed 4 years ago

alexpiper commented 4 years ago

Add an example of fetching mitochondrial genomes and using cleanseqs to pull out the COI gene to vignette.

alexpiper commented 4 years ago

Added option of marker="mitogenome" to fetchSeqs when DB="genbank". This will download full mitochondrial genomes only by implementing the filter 'AND mitochondrion[filter] AND genome'. The PHMM used in the clean_seqs function will extract the target loci from the mitogenome.

Added example of this to the main vignette.