An efficient pipeline for ancient DNA mapping and recovery of endogenous ancient DNA from whole‐genome sequencing data

Autor: Wenhao Xu, Yu Lin, Keliang Zhao, Haimeng Li, Yinping Tian, Jacob Njaramba Ngatia, Yue Ma, Sunil Kumar Sahu, Huabing Guo, Xiaosen Guo, Yan Chun Xu, Huan Liu, Karsten Kristiansen, Tianming Lan, Xinying Zhou

Publikováno v: Ecology and Evolution, Vol 11, Iss 1, Pp 390-401 (2021)

Abstract Ancient DNA research has developed rapidly over the past few decades due to improvements in PCR and next‐generation sequencing (NGS) technologies, but challenges still exist. One major challenge in relation to ancient DNA research is to re

Externí odkaz: https://doaj.org/article/9a0141321c6e4bf783df74671cc6a512

An efficient pipeline for ancient DNA mapping and recovery of endogenous ancient DNA from whole‐genome sequencing data

Autor: Xinying Zhou, Keliang Zhao, Yue Ma, Yu Lin, Huabing Guo, Yinping Tian, Guo Xiaosen, Huan Liu, Karsten Kristiansen, Yan Chun Xu, Sunil Kumar Sahu, Tianming Lan, Jacob Njaramba Ngatia, Haimeng Li, Wenhao Xu

Publikováno v: Ecology and Evolution
Xu, W, Lin, Y, Zhao, K, Li, H, Tian, Y, Ngatia, J N, Ma, Y, Sahu, S K, Guo, H, Guo, X, Xu, Y C, Liu, H, Kristiansen, K, Lan, T & Zhou, X 2021, ' An efficient pipeline for ancient DNA mapping and recovery of endogenous ancient DNA from whole-genome sequencing data ', Ecology and Evolution, vol. 11, no. 1, pp. 390-401 . https://doi.org/10.1002/ece3.7056
Ecology and Evolution, Vol 11, Iss 1, Pp 390-401 (2021)

Ancient DNA research has developed rapidly over the past few decades due to improvements in PCR and next‐generation sequencing (NGS) technologies, but challenges still exist. One major challenge in relation to ancient DNA research is to recover gen

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bd9caa8ff910601955485df06274ef26
http://europepmc.org/articles/PMC7790629

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

Autor: Anders Götherström, Catarina Ginja, Cindy Sarmento, Gülşah Merve Kılınç, Nuno A. Fonseca, Ana Elisabete Pires, Silvia Guimaraes

Publikováno v: Practical Applications of Computational Biology & Bioinformatics, 15th International Conference (PACBB 2021) ISBN: 9783030862572
PACBB
Digital.CSIC. Repositorio Institucional del CSIC
instname

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 f

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1c9238c1907364b45a864eb3786f17c2
https://doi.org/10.1007/978-3-030-86258-9_11

VC@Scale: Scalable and high-performance variant calling on cluster environments

Autor: Ahmad, T., Al-Ars, Z., Hofstee, H.P.

Publikováno v: GigaScience, 10(9)

Background Recently many new deep learning–based variant-calling methods like DeepVariant have emerged as more accurate compared with conventional variant-calling algorithms such as GATK HaplotypeCaller, Sterlka2, and Freebayes albeit at higher com

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=narcis______::c9128f56d1965c67c340f36ce4a25f40
http://resolver.tudelft.nl/uuid:35a585a6-1a37-4c87-b4c4-b608655b0e17

PipeMEM: A Framework to Speed Up BWA-MEM in Spark with Low Overhead

Autor: Lingqi Zhang, Shoubin Dong, Cheng Liu

Publikováno v: Genes
Volume 10
Issue 11
Genes, Vol 10, Iss 11, p 886 (2019)

(1) Background: DNA sequence alignment process is an essential step in genome analysis. BWA-MEM has been a prevalent single-node tool in genome alignment because of its high speed and accuracy. The exponentially generated genome data requiring a mult

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c1320eb5c651f7c68cb1ff86457c14ba