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 Ace pyrotag pipeline...

 Copyright (C) 2011 Michael Imelfort and Paul Dennis
    
 This program comes with ABSOLUTELY NO WARRANTY;
 This is free software, and you are welcome to redistribute it
 under certain conditions: See the source for more details.

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This is a collection of PERL wrappers which wrap QIIME. uclust and acacia
to perform basic QA and results analysis for 16S rRNA pyrotag datasets

Also contained in this package is a set of scripts for taking information generated
using PyroDB and doing a number of useful things such as sorting reads into folders
and generating csv files for dilition using an epi pipette robot.

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 -- OVERVIEW OF FILES
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./
app_convert.pl                                  # CONVERT A CALIPER PRODUCED PEAKS CSV FILE INTO APP CONCENTRATION FORMAT
app_csv2epi.pl                                  # CONVERT AN APP CONCENTRATION CSV FILE INTO A FORMAT SUITABLE FOR THE EPI PIPETTE ROBOT

app_munge_sff.pl                                # SPLIT AN SFF FILE INTO JOB FOLDERS

app_do_QA.pl                                    # DENOISE AND DE-CHIME A SET OF RAW READS
app_combine.pl                                  # COMBINE SAMPLES FROM MULTIPLE JOBS
app_make_results.pl                             # RUN THE QIIME PIPELINE
app_make_images.pl				# DO PCA etc. AND MAKE IMAGES

app_normalise_reads.pl                          # TAKE A SUBSET OF READS IN A FILE
app_acacia.config				# DEFAULT CONFIG FOR RUNNING ACACIA
README						# THIS FILE

./lib
AppConfig.pm					# COMMON ROUTINES AND MANY DEFAULT PARAMETERS