-
Notifications
You must be signed in to change notification settings - Fork 9
Home
Welcome to the getMito wiki!
Python3 and the conda- and pip-installable click package
From a user-provided list of genera/species/subspecies, getMito extracts the corresponding GenBank accession numbers of their 12S rRNA sequences (reference file: 12S.ref.tsv; available in GitHub repository), cytochrome c oxidase subunit I (reference file: COI.ref.tsv), or mitochondrial sequences (reference file: mitofish.ref.tsv), if available. Refer to Section 4 and its subsections for more information on these reference databases.
getSeq is a companion script to getMito to fetch sequences from a getMito output file or a list of accession numbers. Sequence reference files are stored as python pickle dumps and include mitofish.pickle, 12S.pickle, and COI.pickle. Refer to Section 4, specifically Section 4.6, for more information how the sequence reference files are created.
getTaxa is a companion script to getMito to fetch genus/species/subspecies belonging to a specified list of taxonomic categories (subfamily/family/order/class/phylum) using eukaryotic data from NCBI Taxonomy (reference file: eukaryota.tsv. The *.txt output can then be used as input for getMito. Refer to Section 4.7 for more information on the reference database.