Title: pyfaidx: efficient pythonic random access to fasta subsequences

Type Software Shirley, Matthew (2014): pyfaidx: efficient pythonic random access to fasta subsequences. Zenodo. Software. https://zenodo.org/record/8548

Author: Shirley, Matthew (Johns Hopkins School of Medicine) ;

Links

• Item record in Zenodo
• Digital object URL

Summary

Samtools provides a function "faidx" (FAsta InDeX), which creates a small flat index file ".fai" allowing for fast random access to any subsequence in the indexed fasta, while loading a minimal amount of the file in to memory.

Pyfaidx provides an interface for creating and using this index for fast random access of DNA subsequences from huge fasta files in a "pythonic" manner. Indexing speed is comparable to samtools, and in some cases sequence retrieval is much faster.

https://github.com/mdshw5/pyfaidx

More information

• DOI: 10.5281/zenodo.8548

Subjects

• fasta, sequence retrieval

Dates

• Publication date: 2014
• Issued: March 24, 2014

Rights

• https://opensource.org/licenses/MIT MIT License
• info:eu-repo/semantics/openAccess Open Access

Format

electronic resource

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