Create 2bit Database for Faster BLAT Searching

Included with the BLAT source code is a useful utility that converts FASTA references to 2bit format.  The utility, faToTwoBit, works simply by providing the original reference .fa file to be converted to a .2bit file.  Here is the syntax to run the program:

faToTwoBit in.fa [in2.fa in3.fa ...] out.2bit

view raw faToTwoBit.sh hosted with ❤ by GitHub

A few simple options are also included:
-noMask
-stripVersion
-ignoreDups

For more details on these options, type faToTwoBit at the command line.  Hope this 2bit reference database speeds up your BLAT searches!