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3 results on '"Götherström, Anders [0000-0001-8579-1304]"'

1. A Study on Burrows-Wheeler Aligner’s Performance Optimization for Ancient DNA Mapping

Author

Sarmento, Cindy [0000-0003-1762-500X], Guimarães, Silvia [0000-0002-3778-3315], Kılınç, Gülşah Merve [0000-0002-2024-3910], Götherström, Anders [0000-0001-8579-1304], Pires, Ana Elisabete [0000-0002-1118-8569], Ginja, Catarina [0000-0003-2278-7089], Fonseca, Nuno A. [0000-0003-4970-7288], Sarmento, Cindy, Guimarães, Silvia, Kılınç, Gülşah Merve, Götherström, Anders, Pires, Ana Elisabete, Ginja, Catarina, Fonseca, Nuno A., Sarmento, Cindy [0000-0003-1762-500X], Guimarães, Silvia [0000-0002-3778-3315], Kılınç, Gülşah Merve [0000-0002-2024-3910], Götherström, Anders [0000-0001-8579-1304], Pires, Ana Elisabete [0000-0002-1118-8569], Ginja, Catarina [0000-0003-2278-7089], Fonseca, Nuno A. [0000-0003-4970-7288], Sarmento, Cindy, Guimarães, Silvia, Kılınç, Gülşah Merve, Götherström, Anders, Pires, Ana Elisabete, Ginja, Catarina, and Fonseca, Nuno A.

Abstract

The high levels of degradation characteristic of ancient DNA molecules severely hinder the recovery of endogenous DNA fragments and the discovery of genetic variation, limiting downstream population analyses. Optimization of read mapping strategies for ancient DNA is therefore essential to maximize the information we are able to recover from archaeological specimens. In this paper we assess Burrows-Wheeler Aligner (BWA) effectiveness for mapping of ancient DNA sequence data, comparing different sets of parameters and their effect on the number of endogenous sequences mapped and variants called. We also consider different filtering options for SNP calling, which include minimum values for depth of coverage and base quality in addition to mapping quality. Considering our results, as well as those of previous studies, we conclude that BWA-MEM is a good alternative to the current standard BWA-backtrack strategy for ancient DNA studies, especially when the computational resources are limited and time is a constraint.

Published
2021

2. Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets

Author

Swedish Research Council, European Commission, Stockholm University, Feuerborn, Tatiana R. [0000-0003-1610-3402], Palkopoulou, Eleftheria [0000-0001-7382-7509], van der Valk, Tom [0000-0001-6582-3452], von Seth, Johanna [0000-0002-1324-7489], Munters, Arielle R. [0000-0003-1512-6565], Pečnerová, Patrícia [0000-0001-9350-1987], Dehasque, Marianne [0000-0002-4640-8306], Ureña, Irene [0000-0001-9724-9977], Ersmark, Erik [0000-0003-4186-7498], Krzewińska, Maja [0000-0002-6702-8724], Rodríguez-Varela, Ricardo [0000-0002-4173-8648], Götherström, Anders [0000-0001-8579-1304], Dalén, Love [0000-0001-6307-8188], Díez-Del-Molino, David [0000-0002-9701-5940], Feuerborn, Tatiana R., Palkopoulou, Eleftheria, van der Valk, Tom, von Seth, Johanna, Munters, Arielle R., Pečnerová, Patrícia, Dehasque, Marianne, Ureña, Irene, Ersmark, Erik, Lagerholm, Vendela Kempe, Krzewińska, Maja, Rodríguez-Varela, Ricardo, Götherström, Anders, Dalén, Love, Díez-Del-Molino, David, Swedish Research Council, European Commission, Stockholm University, Feuerborn, Tatiana R. [0000-0003-1610-3402], Palkopoulou, Eleftheria [0000-0001-7382-7509], van der Valk, Tom [0000-0001-6582-3452], von Seth, Johanna [0000-0002-1324-7489], Munters, Arielle R. [0000-0003-1512-6565], Pečnerová, Patrícia [0000-0001-9350-1987], Dehasque, Marianne [0000-0002-4640-8306], Ureña, Irene [0000-0001-9724-9977], Ersmark, Erik [0000-0003-4186-7498], Krzewińska, Maja [0000-0002-6702-8724], Rodríguez-Varela, Ricardo [0000-0002-4173-8648], Götherström, Anders [0000-0001-8579-1304], Dalén, Love [0000-0001-6307-8188], Díez-Del-Molino, David [0000-0002-9701-5940], Feuerborn, Tatiana R., Palkopoulou, Eleftheria, van der Valk, Tom, von Seth, Johanna, Munters, Arielle R., Pečnerová, Patrícia, Dehasque, Marianne, Ureña, Irene, Ersmark, Erik, Lagerholm, Vendela Kempe, Krzewińska, Maja, Rodríguez-Varela, Ricardo, Götherström, Anders, Dalén, Love, and Díez-Del-Molino, David

Abstract

After over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data.

Published
2020

3. A Study on Burrows-Wheeler Aligner’s Performance Optimization for Ancient DNA Mapping

Author

Anders Götherström, Catarina Ginja, Cindy Sarmento, Gülşah Merve Kılınç, Nuno A. Fonseca, Ana Elisabete Pires, Silvia Guimaraes, Sarmento, Cindy, Guimarães, Silvia, Kılınç, Gülşah Merve, Götherström, Anders, Pires, Ana Elisabete, Ginja, Catarina, Fonseca, Nuno A., Sarmento, Cindy [0000-0003-1762-500X], Guimarães, Silvia [0000-0002-3778-3315], Kılınç, Gülşah Merve [0000-0002-2024-3910], Götherström, Anders [0000-0001-8579-1304], Pires, Ana Elisabete [0000-0002-1118-8569], Ginja, Catarina [0000-0003-2278-7089], and Fonseca, Nuno A. [0000-0003-4970-7288]

Subjects
education.field_of_study, Ancient DNA, Burrows–Wheeler transform, Computer science, Population, BWA-MEM, Limiting, computer.software_genre, Constraint (information theory), Data sequences, BWA-aln, Variant calling, Genetic variation, Data mining, education, computer, Alignment
Abstract

The high levels of degradation characteristic of ancient DNA molecules severely hinder the recovery of endogenous DNA fragments and the discovery of genetic variation, limiting downstream population analyses. Optimization of read mapping strategies for ancient DNA is therefore essential to maximize the information we are able to recover from archaeological specimens. In this paper we assess Burrows-Wheeler Aligner (BWA) effectiveness for mapping of ancient DNA sequence data, comparing different sets of parameters and their effect on the number of endogenous sequences mapped and variants called. We also consider different filtering options for SNP calling, which include minimum values for depth of coverage and base quality in addition to mapping quality. Considering our results, as well as those of previous studies, we conclude that BWA-MEM is a good alternative to the current standard BWA-backtrack strategy for ancient DNA studies, especially when the computational resources are limited and time is a constraint., This work received funding from: the project PORBIOTA- Portuguese E-Infrastructure for Information and Research on Biodiversity (POCI-01-0145-FEDER-022127), supported by Operational Thematic Program for Competitiveness and Internationalization (POCI), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (FEDER); Fundação Nacional para a Ciência e a Tecnologia (FCT), Portugal, contract grant 2020.02754.CEECIND (C.G.), Norma Transitória contract grant DL 57/2016/CP1440/CT0029 (A.E.P.) and the ARCHAIC Project grant PTDC/CVTLIV/2827/2014 co-funded by COMPETE 2020 POCI-01-0145-FEDER-016647 and LISBOA-01-0145-FEDER-016647 (C.G.). This work was also supported by National Funds through FCT/MCTES under the UIDB/50027/2020 funding.

Published
2021
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