AuthentiCT: a model of ancient DNA damage to estimate the proportion of present-day DNA contamination
Abstract Contamination from present-day DNA is a fundamental issue when studying ancient DNA from historical or archaeological material, and quantifying the amount of contamination is essential for downstream analyses. We present AuthentiCT, a command-line tool to estimate the proportion of present-...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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BMC
2020-09-01
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| Series: | Genome Biology |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13059-020-02123-y |
| _version_ | 1819290006429106176 |
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| author | Stéphane Peyrégne Benjamin M. Peter |
| author_facet | Stéphane Peyrégne Benjamin M. Peter |
| author_sort | Stéphane Peyrégne |
| collection | DOAJ |
| description | Abstract Contamination from present-day DNA is a fundamental issue when studying ancient DNA from historical or archaeological material, and quantifying the amount of contamination is essential for downstream analyses. We present AuthentiCT, a command-line tool to estimate the proportion of present-day DNA contamination in ancient DNA datasets generated from single-stranded DNA libraries. The prediction is based solely on the patterns of post-mortem damage observed on ancient DNA sequences. The method has the power to quantify contamination from as few as 10,000 mapped sequences, making it particularly useful for analysing specimens that are poorly preserved or for which little data is available. |
| first_indexed | 2024-12-24T03:15:53Z |
| format | Article |
| id | doaj.art-4eea26778ce148668fc12daa0510dd44 |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-12-24T03:15:53Z |
| publishDate | 2020-09-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-4eea26778ce148668fc12daa0510dd442022-12-21T17:17:38ZengBMCGenome Biology1474-760X2020-09-0121111610.1186/s13059-020-02123-yAuthentiCT: a model of ancient DNA damage to estimate the proportion of present-day DNA contaminationStéphane Peyrégne0Benjamin M. Peter1Department of Evolutionary Genetics, Max Planck Institute for Evolutionary AnthropologyDepartment of Evolutionary Genetics, Max Planck Institute for Evolutionary AnthropologyAbstract Contamination from present-day DNA is a fundamental issue when studying ancient DNA from historical or archaeological material, and quantifying the amount of contamination is essential for downstream analyses. We present AuthentiCT, a command-line tool to estimate the proportion of present-day DNA contamination in ancient DNA datasets generated from single-stranded DNA libraries. The prediction is based solely on the patterns of post-mortem damage observed on ancient DNA sequences. The method has the power to quantify contamination from as few as 10,000 mapped sequences, making it particularly useful for analysing specimens that are poorly preserved or for which little data is available.http://link.springer.com/article/10.1186/s13059-020-02123-yContaminationAncient DNADeaminationDamage patterns |
| spellingShingle | Stéphane Peyrégne Benjamin M. Peter AuthentiCT: a model of ancient DNA damage to estimate the proportion of present-day DNA contamination Genome Biology Contamination Ancient DNA Deamination Damage patterns |
| title | AuthentiCT: a model of ancient DNA damage to estimate the proportion of present-day DNA contamination |
| title_full | AuthentiCT: a model of ancient DNA damage to estimate the proportion of present-day DNA contamination |
| title_fullStr | AuthentiCT: a model of ancient DNA damage to estimate the proportion of present-day DNA contamination |
| title_full_unstemmed | AuthentiCT: a model of ancient DNA damage to estimate the proportion of present-day DNA contamination |
| title_short | AuthentiCT: a model of ancient DNA damage to estimate the proportion of present-day DNA contamination |
| title_sort | authentict a model of ancient dna damage to estimate the proportion of present day dna contamination |
| topic | Contamination Ancient DNA Deamination Damage patterns |
| url | http://link.springer.com/article/10.1186/s13059-020-02123-y |
| work_keys_str_mv | AT stephanepeyregne authentictamodelofancientdnadamagetoestimatetheproportionofpresentdaydnacontamination AT benjaminmpeter authentictamodelofancientdnadamagetoestimatetheproportionofpresentdaydnacontamination |