SNP IDENTIFICATION PIPELINE:

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<= span style=3D'font-family:"Courier New"'> '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 'C= ONSED' 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 insta= lled and configured PHRED, PHRAP, and PolyBayes sepa= rately

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

TRACE FILE PROCESSING using PHRED and P= HRAP 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 f= iles.

3. Sequence files are processed by PHRA= P.

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

folder.

5. Running POLYBAYES: .ACE file is read= by PolyBayes and results of Polybay= es 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 CONS= ED-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