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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