Randomize FASTA

Randomizes FASTA sequence for each input entry

This is a useful way to generate a type of negative control for some sequence analysis that preserves the original dataset's nucleotide frequencies.

File input (FASTA)

This script processes FASTA-type files so make sure your input is properly formatted and uses the appropriate .fa/.fasta/.fsa extension if you are working from the GUI.

Seed Option

Users have the option to set a random seed for reproducible runs.

Output Options (FASTA)

For each input FASTA file, a new shuffled FASTA file is created and named based on the filename of the input with the the following suffix: *_RAND.fa.

Output GZip

Toggling this allows the user to write output to a compressed file format using a general compression (gzip) which has the added advantage of speeding up the execution time by shrinking the I/O load (esp for large output). The .gz extension will be appended as appropriate.

Command Line Interface

Usage:

java -jar ScriptManager.jar sequence-analysis randomize-fasta [-hV] [-o=<output>]
<fastaFile>

Positional Input

Option	Description
<fastaFile>	reference genome FASTA file

Output Options

Option	Description
-o, --output=<output>	specify output directory (name will be same as original with .gff ext)
-z, --gzip	gzip output (default=false)