SNP IDENTIFICATION PIPELINE:

Script name: unix-snp-trace

PURPOSE: Script reads trace data from a folder, process the data

by ‘PHRED’, generates fasta sequences, PHD files, QUAL files.

PHRAP process the fasta sequences and produces ‘.ACE’ file which is read by Polybayes program.

Last part of the script (CONSED) calls 'phredPhrap' script and 'consed'

from 'edit_dir' which is sub folder of 'phrap_out' folder.

'phredPhrap' script and CONSED programs will work if you have installed

and configured 'PHRED/PHRAP/CONSED' under a separate folder as a single

package.

Please comment the lines that invoke 'CONSED' at the bottom of this script if you do not wish to run CONSED.

STEPS INVOLVED

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This script assumes that you have installed and configured PHRED, PHRAP, and PolyBayes separately

Script can be modified to accept a multiple fasta file as input (skipping PHRED analysis)

TRACE FILE PROCESSING using PHRED and PHRAP that are installed under

individual folders.

1. Reads trace data, process and writes output files under

'$HOME/phred_out' directory.

2. Subdirectories under 'phred_out' contains sequences, chromatogram files and PHD files.

3. Sequence files are processed by PHRAP.

4. PHRAP produces contigs, alignment and .ace files under 'phrap_out'

folder.

5. Running POLYBAYES: .ACE file is read by PolyBayes and results of Polybayes are written into 'poly_out'

6. phredPhrap and consed viewer are executed from phred_out/edit_dir using chromatogram files as input;for processing trace data and viewing with CONSED-VIEWER using PHRED/PHRAP/CONSED set of programs

# -------------- OUTPUT FOLDERS ------------

OUTPUTS 1. phred_out, results of PHRED analysis

OUTPUTS 2. phrap_out, results of PHRAP analysis

OUTPUTS 2. poly_out, results of POLYBayes analysis