Assembly Release QA Steps: Difference between revisions
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When a new or updated assembly is ready to QA, the QA team should perform the following steps, outlined in this guide. | When a new or updated assembly is ready to QA, the QA team should perform the following steps, outlined in this guide. | ||
<span style="color:darkgray"> | |||
==Notes about assembly source== | |||
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 | |||
While genbank and refseq assemblies can be claimed to be 'identical' | everything are different, aptMan1 has contig names of the | ||
that just means they use the same sequence. The names for | format NW_013982187v1 which is a RefSeq identifier. | ||
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 | galGal5 is a RefSeq assembly GCF_000002315.4 | ||
It does have the chrM/NC_001323.1 | It does have the chrM/NC_001323.1 | ||
RefSeq assemblies often are delivered with chrMt, although not | RefSeq assemblies often are delivered with chrMt, although not | ||
always (sometimes none exists). Genbank assemblies are almost | always (sometimes none exists). Genbank assemblies are almost | ||
always delivered *without* a chrMt | always delivered *without* a chrMt | ||
RefSeq assemblies are delivered with NCBI gene predictions, Genbank | RefSeq assemblies are delivered with NCBI gene predictions, Genbank | ||
assemblies do *not* have gene predictions. | assemblies do *not* have gene predictions. | ||
Hence, whenever possible it is preferable to use RefSeq assemblies | Hence, whenever possible it is preferable to use RefSeq assemblies | ||
since they have that extra stuff. This is a recent innovation at | since they have that extra stuff. This is a recent innovation at | ||
UCSC, we (==I) always used to use GenBank assemblies because I was | UCSC, we (==I) always used to use GenBank assemblies because I was | ||
under the mistaken impression that somehow that was the gold standard | under the mistaken impression that somehow that was the gold standard | ||
'official' assembly. Not true at all. Live and learn, however slowly.< | 'official' assembly. Not true at all. Live and learn, however slowly. | ||
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Revision as of 16:10, 18 October 2016
Welcome to the Assembly Release: QA Guide 😀
Page created Fall. 2016 by Cath, Jairo, and ChrisV.
This page is currently a draft in progress.
For now, use Releasing_an_assembly instead.
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.
CHANGE HAPPENS.
As time goes on, please update this section as things change!
For the UCSC Genome Browser QA Team, there are two types of genome assemblies:
- 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.
Notes about assembly source
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
