cite hg19/Grch37

[Rose Fröhlich]

Hello Matthew,

thanks again for your help. So do I understand you correctly that I can cite the same paper for hg19 UCSC and Grch37 of the NCBI? And that I do need to cite a paper wen referring to the reference genome, even the though the data was used in a variant call programm (such as the tst170 web app or a programm in the qiagen gen globe analysis center) but not directly by myself?

As I said earlier, I  do not know which assembly was used in the programms, as this was to specified in the programme or output files. So in case I should cite UCSC hg19, which of the papers should be cited (information from http://genome-euro.ucsc.edu/cite.html):

Human genome assembly: The Genome Sequencing Consortium. Initial sequencing and analysis of the human genome.  Nature. 2001 Feb 15;409(6822):860-921.

Very early human genome assemblies: Kent WJ, Haussler D. Assembly of the working draft of the human genome with gigAssembler. Genome Res. 2001 Sep;11(9)1541-1548. (Cite this paper when publishing results pertaining to human genome assemblies prior to the 22 Dec. 2001 assembly.)

Or should I only cite the following paper, as stated on the website you mentioned (https://www.ncbi.nlm.nih.gov/grc/help/faq/#how-to-cite):

https://pubmed.ncbi.nlm.nih.gov/21750661/

Thanks again for your help!

All the best,

Rose

[Luis Nassar]

Hello, Rose.

It should be acceptable to just cite the GRCh37/hg19 paper described at the NCBI site (https://www.ncbi.nlm.nih.gov/grc/help/faq/#how-to-cite) if that was the human assembly used.

Then, as far as the Genome Browser and its tools (and cytoband track), you could cite our latest publication:

https://academic.oup.com/nar/article/49/D1/D1046/5998393

As well as the references at the bottom of the cytoband data track, as my colleague mentioned: http://genome-euro.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=cytoBand

I hope this is helpful. Please include genom...@soe.ucsc.edu in any replies to ensure visibility by the team.

Lou Nassar
UCSC Genomics Institute

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