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

samiare

cmod

/*  

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  1. Make a Fluid (http://fluidapp.com/) instance of https://facebook.com/messages/
  1. a. (You need to buy the paid version of Fluid to modify UserStyles)
  2. Apply the below CSS as a Userstyles stylesheet
  3. Like magic, you can now message without all the cruft of Full Facebook
  

lh3

References:

• https://support.basespace.illumina.com/knowledgebase/articles/403618-python-run-downloader
• https://developer.basespace.illumina.com/docs/content/documentation/rest-api/api-reference

Steps:

1. Follow steps 1-5 in the first link above to acquire access_token. This will take a while, but you only need to do this once. Never share this token!!
2. Find the file you want to download. Copy the link, which looks something like: https://basespace.illumina.com/sample/9804795/files/tree/NA12878-L1_S1_L001_R1_001.fastq.gz?id=515013503. The "id" is the unique file identifier.
3. Download the file with: wget -O filename 'https://api.basespace.illumina.com/v1pre3/files/{id}/content?access_token={token}', where {token} is from step 1 and {id} from step 2.

ngcrawford

#!/usr/bin/env python
# encoding: utf-8

import sys
import argparse

def interface():
    parser = argparse.ArgumentParser()

    parser.add_argument('--rm-short-reads',