Written By: David Crabb Eric Triplett's Group University of Florida Last Updated: February 9, 2010

1. Perl and R
2. Input
3. Running PANGEA
4. TaxCollector Database
5. cd-hit-est Installation
6. Chi-Square Tool
7. Changes

Typical Usage:

perl PANGEA4MAC.pl -s inputSequences.fas -q inputSequences.fas.qual -b inputBarcodes.txt -d taxcollector.fas

All parameters:

	-s .fas raw sequence input file
	-q .fas.qual quality input file
	-b .txt file containing barcodes or put "n" for no barcodes
	-d tax collector "isolates only" database file
	-u tax collector "all" database file
	-h input help

PANGEA uses Perl 5 which is available at http://www.perl.org/

The Chi-Square Tool uses R 2, which is available at: http://cran.r-project.org/

Make sure the barcode input file is in the correct format: numbered starting at "01" with a tab between the number and the barcode sequence. Do not put any blank lines after the final barcode. Check the example in the PANGEA folder to see the exact format.

A "-n minimum number of sequences selected.." option is included. Of course, this is not necessary to run the program. It just allows the user to specify if they have a different number of sequences they want for the normalized data to each have. Otherwise, the program automatically sets the minimum at the lowest number a barcode has over 100.

Usage

perl PANGEA4MAC.pl -s inputSequences.fas -q inputSequences.fas.qual -b inputBarcodes.txt -d taxcollector.fas

Before starting PANGEA do not leave any of the files in the PANGEA_output folder open. This will inhibit PANGEA from removing and replacing its output folder and could mess up your output. Instead, rename the previous output folder whatever you want so that data is not lost. If you want to discard that data anyway, then don't rename it and when the program runs it will remove it and put the new data in PANGEA_output.

See TaxCollector on Github for instructions on how to prepare a TaxCollector database.