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Pyfaidx website  

PYFAIDX 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 file, while loading a minimal amount of the file in to memory. This python module implements pure Python classes for indexing, retrieval, and in-place modification of FASTA files using a PYFAIDX compatible index. The pyfaidx module is API compatible with the pygr seqdb module. A command-line script "faidx" is installed alongside the pyfaidx module, and facilitates complex manipulation of FASTA files without any programming knowledge.\\

Environment Modules

Run module spider Pyfaidx to find out what environment modules are available for this application.

System Variables

  • HPC_PYFAIDX_DIR - installation directory


If you publish research that uses Pyfaidx you have to cite it as follows:

Shirley MD, Ma Z, Pedersen B, Wheelan S. Efficient "pythonic" access to FASTA files using pyfaidx. PeerJ PrePrints 3:e1196. 2015.