Processes ancient DNA data that was generated using NGS.

This pipeline employs a best practices approach for taking the data from Raw FASTQ files and creates a number of useful output files.

Run ./install.sh but before running make sure the INSTALL_DIR variable in this script points to a directory that is located on your path.

You will need to change the hardcoded path in rscripts/coverage_script.R

to point to your version of the file rscripts/coverage_plot.R

Python dependencies can be installed by running.

pip install -r requirements.txt

This will install pysam, PyVCF, pyfasta, and Biopython.

Navigate to src/mapDamage/ and follow all installation instructions at http://ginolhac.github.io/mapDamage/.

Navigate to src/seqmagick/ and run python setup.py install

Navigate to src/AdapterRemoval/ and run the following commands.

tar xvzf AdapterRemoval-1.5.4.tar.gz
make

Then ensure that the executable AdapterRemoval is on your path.

Unix tools realpath tool and zcat

All the following executables must be installed, and accesible from your path.

• Muscle (http://www.drive5.com/muscle/)
• R programming language (https://www.r-project.org/) with the packages
  • ggplot2, Biostrings, getopt.
• bwa (http://bio-bwa.sourceforge.net/)
• samtools (http://samtools.github.io/)
• bcftools (https://samtools.github.io/bcftools/)
• parallel (https://www.gnu.org/software/parallel/)

Navigate into the tests/test_data/ directory and run the following commands.

# generate pipeline_setup.txt 
create_pipeline_setup.sh . raw
# run pipeline for human mtDNA. make sure you replace the path to the reference file. 
ancient_pipeline.sh -C "gi|251831106|ref|NC_012920.1|" \
-r ~/Programming/OpenSource/MyGitHub/ancient_dna_pipeline/ref/contamination.fa  \ 
-S "human"  -P 1