is hg3 available anywhere?

[Martin Krzywinski]

I'm creating an information graphic based on historical assemblies.

I've been able to download all human genome assemblies listed here

https://genome.ucsc.edu/FAQ/FAQreleases.html

from this page

https://hgdownload.soe.ucsc.edu/downloads.html#human

but unfortunately hg3 (Jul 2000) does not appear to be available.

Does anyone know whether the hg3 assembly is available anywhere?

Thanks kindly,

m

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

[Hiram Clawson]

Good Afternoon Martin:

Please note these directory names that can be used with the URL:

https://hgdownload.soe.ucsc.edu/goldenPath/

to explore all available archived releases we have for the original
human genome versions.

hg07oct2000_oo21 hg12 hg15june2000 hg18 hg24may2000 hg5 hg8
hg10 hg13 hg16 hg19 hg38 hg6
hg11 hg15 hg17 hg19Patch5 hg4 hg7

There is usually a bigZips/ directory in each of those with some form of fa.gz file.
I don't know if hg3 is there, notes in the source tree indicate it
is 'July 17th'

--Hiram

[Robert Kuhn]

my guess is, you order them by date, then hg# and you get:

hg24may2000 

hg15june2000         

hg07oct2000_oo21 

hg4          

hg5  

hg6

hg7

hg8
hg10             

hg11             

hg12 

hg13 
hg15 

hg16         

hg17         

hg18 

hg19        

hg19Patch5 

hg38        

hg07oct2000_oo21 = hg3 ?

        --b0b kuhn

      ucsc genome bioinformatics group

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[Martin Krzywinski]

Unfortunately, hg07oct2000_oo21 doesn't look like hg3, from the bigZips/README.txt

---

This directory contains the preliminary assembly of the Oct. 7, 2000 Genbank freeze
posted on our public site on November 10, 2000. This assembly was updated January 9
2001, and that final assembly of the October freeze is currently posted at
http://genome.ucsc.edu.

---

suggests it's newer than hg4.

It seems that hg3 is AWOL.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

[Brian Lee]

Dear Martin,

It does appear that the hgw3 named assembly is not available anywhere. The versions were rapidly changing at that time as noted by the email from b0b Kuhn.

hg24may2000
hg15june2000
hg07oct2000_oo21
hg4
...

While this statement is not definitive, it appears perhaps the hg[1-9] naming system was implemented right around the hgw3 period to help be more clear about which version was being referred to at UCSC.

All the best,

To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAOZLXSnioD1RjV8RTb_G7YvaGyjMoWsi%3DFAuka9qReNa1bVz%3DQ%40mail.gmail.com.

[Martin Krzywinski]

Many thanks.

m

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca