https://github.com/adamtaranto/low-mem-genomics

Low memory methods for genomic software development
https://github.com/adamtaranto/low-mem-genomics

Last synced: about 2 months ago
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Low memory methods for genomic software development

• Host: GitHub
• URL: https://github.com/adamtaranto/low-mem-genomics
• Owner: Adamtaranto
• License: gpl-3.0
• Created: 2024-03-18T01:51:33.000Z (10 months ago)
• Default Branch: main
• Last Pushed: 2024-03-19T01:19:42.000Z (10 months ago)
• Last Synced: 2024-10-13T20:45:33.214Z (3 months ago)
• Size: 16.6 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# Low Memory Genomics

Low memory methods for genomic software development or "non-microbes have genomes too".

Potential topics:

- Piping output (read mapping example)

- Reading input from stdin in python (softclip example)

- Biopython SeqIO parsing 

- Indexing with pyfai

- Dask for splitting up jobs

- Polars for pandas on disk

- SQLite from python