Ancient DNA data analysis software tools | Whole-genome sequencing
Research involving ancient DNA (aDNA) has experienced a true technological revolution in recent years through advances in the recovery of aDNA and, particularly, through applications of high-throughput sequencing.
Computes nucleotide misincorporation and fragmentation patterns using next-generation sequencing reads mapped against a reference genome. mapDamage 2.0 that extends the original features of mapDamage by incorporating a statistical model of DNA damage.
Removes the adaptors and reconstructs the original DNA sequences. leeHom is based on a Bayesian maximum a posteriori probability approach and process reconstruction for both simulated and ancient DNA data sets. It proceeds by considering the processes of adaptor trimming and merging into a single probabilistic model. This software can handle common sequencing problems like missing cycles and it tends to avoid false positives.
A flexible and user-friendly pipeline applicable to both modern and ancient genomes, which largely automates the in silico analyses behind whole-genome resequencing. PALEOMIX is compatible with a full range of sequence data and performs a series of user-defined analyses, including read trimming, collapsing of overlapping mate-pairs, read mapping, PCR duplicate removal, SNP calling, and metagenomic profiling.
An iterative approach to jointly estimate present-day human contamination in ancient human DNA datasets and reconstruct the endogenous mitochondrial genome. By using sequence deamination patterns and fragment length distributions, schmutzi accurately reconstructs the endogenous mitochondrial genome sequence even when contamination exceeds 50 %. Given sufficient coverage, schmutzi also produces reliable estimates of contamination across a range of contamination rates.
A framework for evaluating the likelihood of a sequence originating from a model with postmortem degradation-summarized in a postmortem degradation score-which allows the identification of DNA fragments that are unlikely to originate from present day sources. PMDtools opens up the potential for genomic analysis of contaminated fossil material.
Permits next-generation sequencing (NGS) analysis to reconstruct ancient genomes. EAGER is able to perform several raw read pre-processing steps, including the initial analysis of raw sequencing reads using FastQC to assess the basic quality of the generated NGS data. It can be used to generate summary reports with the most important statistics including mapping and genotyping of all processed samples.
The basic idea of this program is to align DNA sequencing fragments (shotgun or targeted resequencing) to a reference, then call a consensus. Then the consensus is used as new reference and the process is repeated until convergence. Since it was originally designed to be used on ancient DNA, it supports a position specific substitution matrix, which improves both alignment and consensus calling on chemically damaged aDNA. MIA has been used to assemble a number of Neandertal and early modern human mitochondria.