gargammel: a sequence simulator for ancient DNA

Publikation: Bidrag til tidsskriftTidsskriftartikelfagfællebedømt

Dokumenter

Ancient DNA has emerged as a remarkable tool to infer the history of extinct species and past populations. However, many of its characteristics, such as extensive fragmentation, damage and contamination, can influence downstream analyses. To help investigators measure how these could impact their analyses in silico, we have developed gargammel, a package that simulates ancient DNA fragments given a set of known reference genomes. Our package simulates the entire molecular process from post-mortem DNA fragmentation and DNA damage to experimental sequencing errors, and reproduces most common bias observed in ancient DNA datasets.

AVAILABILITY AND IMPLEMENTATION: The package is publicly available on github: https://grenaud.github.io/gargammel/ and released under the GPL.

CONTACT: gabriel.renaud@snm.ku.dkSupplementary information: Supplementary data are available at Bioinformatics online.

OriginalsprogEngelsk
TidsskriftBioinformatics
Vol/bind33
Udgave nummer4
Sider (fra-til)577-579
Antal sider3
ISSN1367-4803
DOI
StatusUdgivet - 2017

Antal downloads er baseret på statistik fra Google Scholar og www.ku.dk


Ingen data tilgængelig

ID: 172510576