Assembly Release QA Steps: Difference between revisions
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===<span style="color:blue"> | ===<span style="color:blue">Assembly notes=== | ||
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Assemblies/sequences, from various organizations, are submitted to the mother ship [https://www.ncbi.nlm.nih.gov/genbank/ GenBank].<br> | |||
Assemblies/sequences are submitted to the mother ship [https://www.ncbi.nlm.nih.gov/genbank/ GenBank].<br> | |||
Those assemblies [https://www.ncbi.nlm.nih.gov/assembly/help/anomnotrefseq/ might be included in RefSeq if criteria are met]. | Those assemblies [https://www.ncbi.nlm.nih.gov/assembly/help/anomnotrefseq/ might be included in RefSeq if criteria are met]. | ||
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For the UCSC Genome Browser, it is preferable to use RefSeq assemblies (in part due to 'more data'). | For the UCSC Genome Browser, it is preferable to use RefSeq assemblies (in part due to 'more data'). | ||
This is a "learn as we go" direction; historically GeneBank was preferred. | This is a "learn as we go" direction; historically GeneBank was preferred. | ||
Note: [http://www.nature.com/nrg/journal/v13/n5/full/nrg3174.html Nature, 2012 A beginner's guide to eukaryotic genome annotation] | |||
Revision as of 20:31, 24 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.
Introduction
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.
There are two types of assemblies that the QA team will process:
- New species
- New version for existing species
Change happens
Collaboration rocks. Keep me updated!
Think of when you were new to the job - update the wiki with your poor, floundering, confused, past-self in mind.
Don't hesitate to edit this puppy.
Editing this wiki will bring gaggles of glittery giggling unicorn-riding leprechauns to you, and they will improvise a dope rap about you that would make Snoop Dog jelly.
Assembly notes
Assemblies/sequences, from various organizations, are submitted to the mother ship GenBank.
Those assemblies might be included in RefSeq if criteria are met.
- RefSeq assemblies:
- use accession ID: GCF_000002315.4 (e.g., galGal5)
- are delivered with chrMt (if they exisit)
- are delivered with NCBI gene predictions
- Genbank assemblies:
- use accession ID: GCA_000001305.2
- delivered without a chrMt.
- do not have gene predictions.
For the UCSC Genome Browser, it is preferable to use RefSeq assemblies (in part due to 'more data').
This is a "learn as we go" direction; historically GeneBank was preferred.
Note: Nature, 2012 A beginner's guide to eukaryotic genome annotation
🔵 Ready to get started? Let's go to Assembly QA Part 1: DEV Steps
