max-mapper

# 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

fransua

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

darencard

Please see the most up-to-date version of this protocol on my blog at https://darencard.net/blog/.

Genome Annotation using MAKER

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.

Software & Data

Software prerequisites:

1. RepeatModeler and RepeatMasker with all dependencies (I used NCBI BLAST) and RepBase (ver

sujaikumar

Goal

• To create UniRef90 protein databases for NCBI blast and Diamond Blast
• To create a tab delimited taxid mapping file with two columns : sequenceID\tNCBITaxonID

Steps:

Download the uniref90 xml file first (warning - this is ~15 GB, will take a while)