arXiv Open Access 2020

Computational Performance of a Germline Variant Calling Pipeline for Next Generation Sequencing

Jie Liu Xiaotian Wu Kai Zhang Bing Liu Renyi Bao +6 lainnya

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Abstrak

With the booming of next generation sequencing technology and its implementation in clinical practice and life science research, the need for faster and more efficient data analysis methods becomes pressing in the field of sequencing. Here we report on the evaluation of an optimized germline mutation calling pipeline, HummingBird, by assessing its performance against the widely accepted BWA-GATK pipeline. We found that the HummingBird pipeline can significantly reduce the running time of the primary data analysis for whole genome sequencing and whole exome sequencing while without significantly sacrificing the variant calling accuracy. Thus, we conclude that expansion of such software usage will help to improve the primary data analysis efficiency for next generation sequencing.

Topik & Kata Kunci

q-bio.GN cs.PF

Penulis (11)

Jie Liu

Xiaotian Wu

Kai Zhang

Bing Liu

Renyi Bao

Xiao Chen

Yiran Cai

Yiming Shen

Xinjun He

Jun Yan

Weixing Ji

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APA MLA BibTeX

Liu, J., Wu, X., Zhang, K., Liu, B., Bao, R., Chen, X. et al. (2020). Computational Performance of a Germline Variant Calling Pipeline for Next Generation Sequencing. https://arxiv.org/abs/2004.00991

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Informasi Jurnal

Tahun Terbit: 2020
Bahasa: en
Sumber Database: arXiv
Akses: Open Access ✓