Testing of Alignment Parameters for Ancient Samples: Evaluating and Optimizing Mapping Parameters for Ancient Samples Using the TAPAS Tool

Abstract

High-throughput sequence data retrieved from ancient or other degraded samples has led to unprecedented insights into the evolutionary history of many species, but the analysis of such sequences also poses specific computational challenges. The most commonly used approach involves mapping sequence reads to a reference genome. However, this process becomes increasingly challenging with an elevated genetic distance between target and reference or with the presence of contaminant sequences with high sequence similarity to the target species. The evaluation and testing of mapping efficiency and stringency are thus paramount for the reliable identification and analysis of ancient sequences. In this paper, we present ‘TAPAS’, (Testing of Alignment Parameters for Ancient Samples), a computational tool that enables the systematic testing of mapping tools for ancient data by simulating sequence data reflecting the properties of an ancient dataset and performing test runs using the mapping software and parameter settings of interest. We showcase TAPAS by using it to assess and improve mapping strategy for a degraded sample from a banded linsang (Prionodon linsang), for which no closely related reference is currently available. This enables a 1.8-fold increase of the number of mapped reads without sacrificing mapping specificity. The increase of mapped reads effectively reduces the need for additional sequencing, thus making more economical use of time, resources, and sample material.

Historical DNA as a tool to address key questions in avian biology and evolution: A review of methods, challenges, applications, and future directions

“…The difficulties with mapping hDNA can be more pronounced when using a distantly related reference (Kehlmaier et al, ; Taron, Lell, Barlow, & Paijmans, ), as sequence divergence between the reference and the target sequences can interfere with successful mapping (Taron et al, ). Reducing the stringency of mapping parameters, however, can lead to contaminant sequences being mapped to the reference genome (Taron et al, ), as such, it is important to consider these challenges when optimizing mapping parameters. There are a few existing programs for optimizing mapping conditions and for incorporating sequence error for hDNA samples to improve downstream mapping protocols (Table ).…”

“…This rescaling information can be used to improve downstream mapping of hDNA to a reference genome. The program TAPAS (Taron et al, ) allows for testing of mapping tools for ancient samples by simulating degraded sequence data exhibiting common post‐mortem damage and performing test runs using the mapping software and parameter settings of interest. Lastly, Seitz and Nieselt () present a two‐layer assembly approach to produce de novo assemblies from ancient samples, which may be a viable option if a reference genome is unavailable. Variant calling with low coverage data: Once data are filtered and mapped, variant calling software can be employed to identify single nucleotide polymorphisms (SNPs).…”

“…This step will be most successful with a reference genome from a closely related species. The difficulties with mapping hDNA can be more pronounced when using a distantly related reference (Kehlmaier et al, 2017;Taron, Lell, Barlow, & Paijmans, 2018), as sequence divergence between the reference and the target sequences can interfere with successful mapping (Taron et al, 2018).…”

“…Reducing the stringency of mapping parameters, however, can lead to contaminant sequences being mapped to the reference genome (Taron et al, 2018), as such, it is important to consider these challenges when optimizing mapping parameters. There are a few existing programs for optimizing mapping conditions and for incorporating sequence error for hDNA samples to improve downstream mapping protocols (Table 1) 4.…”

“…The program mapDamage2.0(Jónsson et al, 2013) provides estimates of post-mortem damage and can rescale base quality scores for each sample according to their probability of being damaged. This rescaling information can be used to improve downstream mapping of hDNA to a reference genome.The program TAPAS(Taron et al, 2018) allows for testing of mapping tools for ancient samples by simulating degraded sequence data exhibiting common post-mortem damage and performing test runs using the mapping software and parameter settings of interest. Lastly, Seitz and Nieselt (2017) present a two-layer assembly approach to produce de novo assemblies from ancient samples, which may be a viable option if a reference genome is unavailable.…”