https://github.com/ssi-dk/serum_readfilter

https://github.com/ssi-dk/serum_readfilter

Last synced: 3 days ago
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• Host: GitHub
• URL: https://github.com/ssi-dk/serum_readfilter
• Owner: ssi-dk
• License: gpl-3.0
• Created: 2017-11-28T14:05:26.000Z (almost 7 years ago)
• Default Branch: master
• Last Pushed: 2018-02-19T15:30:39.000Z (over 6 years ago)
• Last Synced: 2023-03-02T02:46:32.995Z (over 1 year ago)
• Language: Python
• Size: 59.8 MB
• Stars: 7
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# serum_readfilter

serum_readfilter is a program designed to filter whole genome sequence data to only obtain reads that may touch your gene's of interest. This is accomplished by creating a database off a set of sequences you want to filter by (ie MLST, resistance genes, etc) and then filtering (via Kraken https://github.com/DerrickWood/kraken or Kaiju https://github.com/bioinformatics-centre/kaiju) the raw reads against this database. By default with Kraken this will filter all reads without 1 k-mer match to the database which can reduce your data set substantially while still retaining almost all options that would normally be a potential match to the database. This is very useful when you want to map reads against a gene or have a large set of data to work with and want to make it more managable.

To use:

serum_readfilter makedb kraken -db  -i 

serum_readfilter runfilter kraken -db  -R1  -R2 

bioRxiv link:

https://www.biorxiv.org/content/early/2018/02/15/266080