UCSC
Description
Kent source utilities are based on the code originally developed by Jim Kent for the UCSC genome browser. They include programs for sorting, splitting, or merging fasta sequences; record parsing and data conversion using GenBank, fasta, nib, and blast data formats; sequence alignment; motif searching; hidden Markov model development; and much more. Library subroutines are available for everything from managing C data structures such as linked lists, balanced trees, hashes, and directed graphs to developing routines for SQL, HTML, or CGI code. Additional library functions are available for biological sequence and data manipulation tasks such as reverse complementation, codon and amino acid lookup and sequence translation, as well as functions specifically designed for extracting, loading, and manipulating data in the UCSC Genome Browser Databases.
Execution Environment and Modules
To use kent with the environment modules system at HPC the following commands are available:
Get module information for ucsc:
$module spider kent
Load the default application module:
$module load kent
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_KENT_DIR - directory where kent is located.