readShuffle.pl $input $output
**What it does**
This tool shuffles sequences in a FASTA file.
The output FASTA will have the same composition of nucleotides, in a random order.
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**Purpose**
Allows the user to create a random "in silico" library for statstical analysis.
Usage example: analyze your original FASTA library, then shuffle the FASTA file and perform the same analysis on the shuffled file (as a control).
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**Example**
Input FASTA file::
>BILLIE_1_FC00042:2:1:1465:771
TTAGAGACTACTGCTGACATTTTCTGTCTCTGATAT
>BILLIE_1_FC00042:2:1:1480:719
CTCGGTGGTAGTTGGCGCACTCCTCTACGATTATAA
>BILLIE_1_FC00042:2:1:1617:999
AATTTAGCTATGCGATAACCAGCCTCTTAATGATGG
Output sequence (nucleotides are in random order)::
>BILLIE_1_FC00042:2:1:1465:771
GACTTAATATTTTTGTTTCGTCTGTAGGCACCATCA
>BILLIE_1_FC00042:2:1:1480:719
GTGCATTGTAGTCGCATTGTCCTGTAGGCACCATCA
>BILLIE_1_FC00042:2:1:1617:999
GATCATTTTGAAAGCTGATTCTGTAGGCACCATCAA