Benchmarking software tools for trimming adapters and merging next-generation sequencing data for ancient DNA

• DOI: 10.3389/fbinf.2023.1260486
• Publication Date: 2023-12-07T13:17:27Z
• Authors: Annette Lien; Leonardo Pestana ...; Louis Kraft; Peter Wad Sackett; Gabriel Renaud
• Keywords: Adapter (computing); Trimming; Benchmarking; Ancient DNA

Ancient DNA is highly degraded, resulting in very short sequences. Reads generated with modern high-throughput sequencing machines are generally longer than ancient molecules, therefore the reads often contain some portion of adaptors. It crucial to remove those adaptors, as they can interfere downstream analysis. Furthermore, overlapping portions when has been read forward and backward (paired-end) be merged correct errors improve quality. Several tools have developed for adapter trimming merging, however, no one attempted evaluate their accuracy potential impact on analyses. Through simulation data, seven commonly used were analyzed ability reconstruct sequences through merging. The exhibit notable differences abilities sequence identify overlap, but most substantial difference observed calculate quality scores bases. Selecting appropriate tool a given project depends several factors, although such fastp shortcomings, whereas others like leeHom outperform other aspects. While choice did not result measurable analyzing population genetics using principal component analysis, it important note that analyses sensitive wrongly or rely significantly impacted by tool.