Bioinformatic Scripts used by George S. Long

The scripts located here have been used for the following projects:

1. Collapse of the mammoth-steppe in central Yukon as revealed by ancient environmental DNA <-- Not cited as repo was created after the paper was published and results were only present in the supplementary materials. Only MapDamageLoop was used
2. Ancient Escherichia coli
3. Ancient Brucella melitensis
4. Permafrost microbial communities follow shifts in vegetation, soils, and megafauna extinctions in Late Pleistocene NW North America

Please note that there are some idiosyncrasies present in the scripts due to the specifics of the machine I'm using (take the Core SNP Phylogeny as an example). You'll need to edit scripts as needed to ensure that they'll work for you.

Ancient Escherichia coli

The order of the scripts used is as follows:

1. AncientQC.sh
2. BWAalnMapping.sh <-- Used to map against the Human Genome (with Dedup Flag)

• MapDamageLoop.sh

3. PanGenomeCreation.sh
4. BWAalnMapping.sh <-- Used to map against the E.coli Genome (with Dedup Flag)

• MapDamageLoop.sh
• CoreSNPPhylogenetics.sh <-- Multiple times for global, A0, and ST4995 phylogenies. Treemmer is ran manually after the fact.

5. Manually merging the de-duplicated digests
6. BWAalnMapping.sh <-- Used to map against the K.aerogenes Genome (with Dedup Flag)

• MapDamageLoop.sh

Note about No Longer Used Folder

These scripts are no longer used for a variety of reasons (either created for testing only or fundamental issues with their underlying programs). They should still work, however, they're not currently being actively maintained.