wtroy2 / mapdamage Goto Github PK

• python3 version 2.2.1

conda install -c bioconda mapdamage2=2.2.1

• python3 version 2.2.1 with R and 4 mandatory packages for the Bayesian inference:

conda install -c bioconda mapdamage2=2.2.1=pyr40_0

• From version 2.2.1 the master branch is requiring python3 as python2 is not supported from 2020-01-01.

Complete documentation, instructions, examples, screenshots and FAQ are available at this address.

mapDamage2 is a computational framework written in Python3 and R, which tracks and quantifies DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.

mapDamage was developed at the Centre for GeoGenetics by the Orlando Group .

If you use this program, please cite the following publication: Jónsson H, Ginolhac A, Schubert M, Johnson P, Orlando L. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 23rd April 2013. doi: 10.1093/bioinformatics/btt193

The original mapDamage1 was published in the following article: Ginolhac A, Rasmussen M, Gilbert MT, Willerslev E, Orlando L. mapDamage: testing for damage patterns in ancient DNA sequences. Bioinformatics 2011 27(15):2153-5 http://bioinformatics.oxfordjournals.org/content/27/15/2153

you can test mapDamage by running:

cd mapDamage/mapdamage/
python3 mp_test.py

should return

Started with the command: /usr/local/bin/mapDamage -i tests/test.bam -r tests/fake1.fasta -d tests/results --no-stats
	Reading from 'tests/test.bam'
	Writing results to 'tests/results/'
pdf tests/results/Fragmisincorporation_plot.pdf generated
additional tests/results/Length_plot.pdf generated
Successful run
.
----------------------------------------------------------------------
Ran 2 tests in 3.357s

OK

Please report bugs and suggest possible improvements on GitHub: https://github.com/ginolhac/mapDamage/issues/new