- To create UniRef90 protein databases for NCBI blast and Diamond Blast
- To create a tab delimited taxid mapping file with two columns : sequenceID\tNCBITaxonID
Download the uniref90 xml file first (warning - this is ~15 GB, will take a while)
Download the uniref90 xml file first (warning - this is ~15 GB, will take a while)
Please see the most up-to-date version of this protocol on my blog at https://darencard.net/blog/.
MAKER is a great tool for annotating a reference genome using empirical and ab initio gene predictions. GMOD, the umbrella organization that includes MAKER, has some nice tutorials online for running MAKER. However, these were quite simplified examples and it took a bit of effort to wrap my head completely around everything. Here I will describe a de novo genome annotation for Boa constrictor in detail, so that there is a record and that it is easy to use this as a guide to annotate any genome.
from itertools import chain | |
from matplotlib.collections import LineCollection | |
from matplotlib import markers | |
from matplotlib.path import Path | |
import numpy as np | |
from ete3 import Tree, NodeStyle |
# in zenodo ui create a deposition. get the id | |
curl -H "Accept: application/json" -H "Authorization: Bearer $TOKEN" "https://www.zenodo.org/api/deposit/depositions/$DEPOSITION" | |
# get the bucket id from above | |
curl --progress-bar -o /dev/null --upload-file ./$FILE https://www.zenodo.org/api/files/$BUCKET/$FILE?access_token=$TOKEN |