fastMitoCalc：一个用于从全基因组序列中估计线粒体DNA拷贝数的超快速程序。
fastMitoCalc: an ultra-fast program to estimate mitochondrial DNA copy number from whole-genome sequences.
作者信息
Qian Yong, Butler Thomas J, Opsahl-Ong Krista, Giroux Nicholas S, Sidore Carlo, Nagaraja Ramaiah, Cucca Francesco, Ferrucci Luigi, Abecasis Gonçalo R, Schlessinger David, Ding Jun
机构信息
Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA.
Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Cagliari, Italy.
出版信息
Bioinformatics. 2017 May 1;33(9):1399-1401. doi: 10.1093/bioinformatics/btw835.
Abstract
AVAILABILITY AND IMPLEMENTATION
fastMitoCalc is available at https://lgsun.irp.nia.nih.gov/hsgu/software/mitoAnalyzer/index.html.
CONTACT
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
可用性与实施
fastMitoCalc可在https://lgsun.irp.nia.nih.gov/hsgu/software/mitoAnalyzer/index.html获取。
联系方式
补充信息
补充数据可在《生物信息学》在线获取。
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本文引用的文献
1
Age-Related and Heteroplasmy-Related Variation in Human mtDNA Copy Number.
PLoS Genet. 2016 Mar 15;12(3):e1005939. doi: 10.1371/journal.pgen.1005939. eCollection 2016 Mar.
2
Genetic Control over mtDNA and Its Relationship to Major Depressive Disorder.
Curr Biol. 2015 Dec 21;25(24):3170-7. doi: 10.1016/j.cub.2015.10.065. Epub 2015 Dec 10.
3
Assessing Mitochondrial DNA Variation and Copy Number in Lymphocytes of ~2,000 Sardinians Using Tailored Sequencing Analysis Tools.
PLoS Genet. 2015 Jul 14;11(7):e1005306. doi: 10.1371/journal.pgen.1005306. eCollection 2015 Jul.
4
Molecular signatures of major depression.
Curr Biol. 2015 May 4;25(9):1146-56. doi: 10.1016/j.cub.2015.03.008. Epub 2015 Apr 23.
5
Mitochondrial DNA copy number is associated with breast cancer risk.
PLoS One. 2013 Jun 12;8(6):e65968. doi: 10.1371/journal.pone.0065968. Print 2013.
6
Quantitative assessment of mitochondrial DNA copies from whole genome sequencing.
BMC Genomics. 2012;13 Suppl 7(Suppl 7):S5. doi: 10.1186/1471-2164-13-S7-S5. Epub 2012 Dec 13.
7
The Sequence Alignment/Map format and SAMtools.
Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8.
8
A prospective study of mitochondrial DNA copy number and risk of non-Hodgkin lymphoma.
Blood. 2008 Nov 15;112(10):4247-9. doi: 10.1182/blood-2008-05-157974. Epub 2008 Aug 18.
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