Overview

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Author: Melanie Schirmer, University of Glasgow, mail@melanieschirmer.com


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### USAGE
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ErrorProfiles_wQ_v1.0.sh <Output_Prefix> <NO_Cores> <file.Calmd> <file.sam> <max_read_length>

The program calculates position and nucleotide-specific error profiles for amplicon datasets
and requires the following input parameters:
    - A prefix for the output files (no whitespaces in prefix). A directory with the same name
      will be created in which the output files are saved. 
    - The number of cores that should be used for the computations.
    - A file with the aligned reads and extended MD tag.
    - A file in sam format with the aligned reads.
    - The maximum read length (e.g. the original length of the sequenced reads).

For additional information and an example see the tutorial in the Test_Dataset directory.  

Additional options:
    -h  shows this help text

Never run multiple copies of the script in the same directory.


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#### DEPENDENCIES
################

Perl             The scripts for the computations are implemented in Perl. (Tested under version v5.10.1.)
                 Ensure that your perl distribution supports:
                   - feature (Perl pragma to enable new features)
                   - Scalar::Util (A selection of general-utility scalar subroutines)

Bash             The main bash script combines the perl scripts and allows to run computation in parallel
GNU parallel     (using GNU parallel).

R                The graphs are generated in R. (Tested under version version 3.0.0.)


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### CITATION 
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Melanie Schirmer, Umer Z. Ijaz, Rosalinda D’Amore, Neil Hall, William T. Sloan and Christopher Quince. Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform. Nucleic Acids Research, 2015.




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### SUPPORT
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If you would like to report a bug, please contact: mail@melanieschirmer.com