README.md

What's this?

This repository includes scripts to obtain files to have fun with the vg tutorial (https://github.com/Pfern/PANGenomics) day 3. Once you have all the files necessary, you can play around bacterial pan-genome.

Requirements

• SRA Toolkit (https://www.ncbi.nlm.nih.gov/sra/docs/toolkitsoft/)
• curl command (if you use wget instead, modify script/fetch_data.sh)
• Jupyter Notebook
• Internet connection since the script downloads several files

How to start

1. Go to scripts/ and run ./fetch_data.sh to obtain E. coli complete genomes, gene tables, and one fastq file as well as minia.
2. Then run run_minia.sh to generate a contig fasta file from the fastq reads.
3. Use extract_gene.ipynb with Jupyter Notebook as necessary. It helps you extract genome regions corresponding to a certain gene from multiple genomes.
4. Now you're free to do whatever you want. Check the original tutorial and have fun.