PMDtools 0.5 – Separating Ancient DNA from Modern Contamination

PMDtools 0.5

:: DESCRIPTION

PMDtools implements a likelihood framework including postmortem damage (PMD), base quality scores and biological polymorphism to allow the identification of degraded DNA sequences that are unlikely to originate from modern contamination.

::DEVELOPER

Jakobsson Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

PMDtools

:: MORE INFORMATION

Citation

P Skoglund, BH Northoff, MV Shunkov, A Derevianko, S Pääbo, J Krause, M Jakobsson (2014)
Separating ancient DNA from modern contamination in a Siberian Neandertal,
Proceedings of the National Academy of Sciences USA doi:10.1073/pnas.1318934111

epiPaleomix – Inference of Ancient DNA Methylation and Nucleosomal Positioning

epiPaleomix

:: DESCRIPTION

epiPaleomix is a Fast, Accurate, and Automatic pipeline for generating nucleosome and methylation maps from high throughput sequencing data underlying ancient samples.

::DEVELOPER

The Centre for Anthropobiology and Genomics of Toulouse

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

epiPaleomix

:: MORE INFORMATION

Citation

Hanghoj K, Seguin-Orlando A, Schubert M, Madsen T, Pedersen JS, Willerslev E, Orlando L.
Fast, Accurate and Automatic Ancient Nucleosome and Methylation Maps with epiPALEOMIX.
Mol Biol Evol. 2016 Dec;33(12):3284-3298. doi: 10.1093/molbev/msw184. Epub 2016 Sep 13. PMID: 27624717; PMCID: PMC5100044.

MapDamage 2.2.1 – Identifies and Quantifies DNA Damage Patterns in Ancient DNA

MapDamage 2.2.1

:: DESCRIPTION

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

::DEVELOPER

The Centre for Anthropobiology and Genomics of Toulouse

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/MacOsX/Linux
Python
R package

:: DOWNLOAD

MapDamage

:: MORE INFORMATION

Citation

Jónsson H, Ginolhac A, Schubert M, Johnson P, Orlando L.
mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters.
Bioinformatics (2013) 29 (13): 1682-1684. doi: 10.1093/bioinformatics/btt193

ANFO 0.98 – Mapper for Ancient DNA

ANFO 0.98

:: DESCRIPTION

Anfo is a mapper in the spirit of Soap/Maq/Bowtie, but its implementation takes more after BLAST/BLAT. It’s most useful for the alignment of sequencing reads where the DNA sequence is somehow modified (think ancient DNA or bisulphite treatment) and/or there is more divergence between sample and reference than what fast mappers will handle gracefully (say the reference genome is missing and a related species is used instead).

::DEVELOPER

Udo Stenzel <udo_stenzel@eva.mpg.de> @ Department of Genetics/Bioinformatics – Max Planck Institut

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Anfo

:: MORE INFORMATION