https://github.com/nvictus/blindex

https://github.com/nvictus/blindex

Last synced: 24 days ago
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• Host: GitHub
• URL: https://github.com/nvictus/blindex
• Owner: nvictus
• Created: 2018-11-24T16:51:51.000Z (about 6 years ago)
• Default Branch: master
• Last Pushed: 2018-11-27T09:26:59.000Z (about 6 years ago)
• Last Synced: 2024-10-03T12:17:50.419Z (3 months ago)
• Size: 31.3 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# assembliotheque

Inspired by https://github.com/dpryan79/ChromosomeMappings.

1. [Find the ftp directory](https://www.ncbi.nlm.nih.gov/genome/doc/ftpfaq/#howtofind) of your favorite reference assembly. The field named "ftp_path" provides the path to the FTP directory containing the data for each assembly. Find the appropriate file with the assembly summary.

* Either the two master assembly summary files:

	- ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_genbank.txt

	- ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_refseq.txt

* Or an assembly summary file for a taxonomic group from the appropriate directory under genbank or refseq. e.g.

	- ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/assembly_summary.txt

* Or an assembly summary file for a species from the appropriate directory under genbank or refseq. e.g.

	- ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/Salmonella_enterica/assembly_summary.txt

2. Take the commented metadata and convert it into a `{assembly}.yaml` file. Normalize the property names to those in GRCh38.

3. Extract the columns in into a `{assembly}` TSV file and normalize the column names to those in GRCh38. If chromosome lengths are not available, you can get them from UCSC and join them into the table.

## Chromosome order

Ordered naturally by chromosome/plasmid.

Fully **assembled** chromosomes/plasmids are followed by **unlocalized** scaffolds, followed by **unplaced** scaffolds, followed by **alt** scaffolds.

## Patch releases

Do not include patch sequences! F that noise.

## TODO

* yaml and table validator scripts