Pyfaidx¶

Description¶

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. If you use pyfaidx in your publication, please cite: Shirley MD, Ma Z, Pedersen B, Wheelan S. Efficient "pythonic" access to FASTA files using pyfaidx. PeerJ PrePrints 3:e1196. 2015.

Environment Modules¶

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

Environment Variables¶

HPC_PYFAIDX_DIR - installation directory
HPC_PYFAIDX_BIN - executable directory

Citation¶

citation¶

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.

Categories¶

biology, ngs, sequencing