Assembly Release QA Steps: Difference between revisions

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== Welcome to the '''Assembly Release: QA Guide''' 😀 ==


{| class=wikitable width=415 align=right
{| class=wikitable width=415 align=right
|
|
:Home: [[Assembly_Release_QA_Steps]]
<span style="color:darkorange">Navigation Menu</span>
#[[Assembly QA Part 1: DEV Steps]]
:[[Assembly_Release_QA_Steps | Home Page]]
#[[Assembly QA Part 2: BETA Steps]]
::[[Assembly QA Part 1 DEV Steps | Assembly QA Part 1: DEV Steps]]
#[[Assembly QA Part 3: RR Steps]]
::[[Assembly QA Part 2 Track Steps | Assembly QA Part 2: Track Steps]]
#[[Assembly QA Part 4: Post Release Steps]]
::[[Assembly QA Part 3 BETA Steps | Assembly QA Part 3: BETA Steps]]
::[[Assembly QA Part 4 RR Steps | Assembly QA Part 4: RR Steps]]
|}
|}


<span style="color:darkred">
Page created Fall. 2016 by Cath, Jairo, and ChrisV. <br>This page is currently a draft in progress.<br>For now, use [[Releasing_an_assembly]] instead.
</span>


<span style="color:olive">See also: [[Releasing_an_assembly | Releasing an assembly (old steps)]] </span>


===<span style="color:blue">Introduction===
</span>


When a developer is ready for a new assembly to be released, the QA team (usually an individual of) will QA and release the assembly. This wiki section exists as a guide for the assembly QA and release process.


 
===<span style="color:dodgerblue">Introduction===
 
===<span style="color:blue">Change happens===
</span>
</span>
As time goes on, please update this section as things change!


When a developer is ready for a new assembly to be released, a member of the QA team will QA and release the assembly. This wiki section exists as a guide for the assembly QA and release process.




For the UCSC Genome Browser QA Team, there are two types of genome assemblies:
The QA rock star can follow this guide in unison with a sync'd Google spreadsheet checklist, simply by copying the [http://genomewiki.ucsc.edu/genecats/index.php/Assembly_QA_Part_1_DEV_Steps#Setup:_Create_a_Google_spreadsheet_checklist_from_a_template super fancy-pants spreadsheet template]. These wiki steps are automatically populated in the spreadsheet as a checklist, and therefore will always be in sync with the wiki.  
# '''New species:''' Assembly for a species that is not already exisiting as a browser.
# '''New version for exisiting species:''' Assembly version for a species that already exists as a browser.


When a new or updated assembly is ready to QA, the QA team should perform the following steps, outlined in this guide.


 
🔵  Ready to get started? Go to  [[Assembly QA Part 1 DEV Steps | Assembly QA Part 1: DEV Steps ]]
===<span style="color:blue">Do storks bring new assemblies in?===
</span>
From Hiram, 10/2016:
 
While genbank and refseq assemblies can be claimed to be 'identical'
that just means they use the same sequence.  The names for
everything are different, aptMan1 has contig names of the
format NW_013982187v1 which is a RefSeq identifier.
 
galGal5 is a RefSeq assembly GCF_000002315.4
It does have the chrM/NC_001323.1
 
RefSeq assemblies often are delivered with chrMt, although not
always (sometimes none exists).  Genbank assemblies are almost
always delivered *without* a chrMt
 
RefSeq assemblies are delivered with NCBI gene predictions, Genbank
assemblies do *not* have gene predictions.
 
Hence, whenever possible it is preferable to use RefSeq assemblies
since they have that extra stuff.  This is a recent innovation at
UCSC, we (==I) always used to use GenBank assemblies because I was
under the mistaken impression that somehow that was the gold standard
'official' assembly.  Not true at all.  Live and learn, however slowly.
 
 
 
 
🔵  Ready to get started? Let's go to  [[Assembly QA Part 1: DEV Steps]]




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[[Category:Browser QA Assembly Release Guide]]
[[Category:Browser QA]]
[[Category:Browser QA]]
[[Category:Browser QA New Assembly]]
[[Category:Browser QA New Assembly]]
[[Category:Browser QA Assembly Release Guide]]

Latest revision as of 23:21, 20 March 2018

Navigation Menu

Home Page
Assembly QA Part 1: DEV Steps
Assembly QA Part 2: Track Steps
Assembly QA Part 3: BETA Steps
Assembly QA Part 4: RR Steps


See also: Releasing an assembly (old steps)


Introduction

When a developer is ready for a new assembly to be released, a member of the QA team will QA and release the assembly. This wiki section exists as a guide for the assembly QA and release process.


The QA rock star can follow this guide in unison with a sync'd Google spreadsheet checklist, simply by copying the super fancy-pants spreadsheet template. These wiki steps are automatically populated in the spreadsheet as a checklist, and therefore will always be in sync with the wiki.


🔵 Ready to get started? Go to Assembly QA Part 1: DEV Steps

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