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SummonChimera Copyright (C) 2014 Joshua Patrick Katz
This program comes with ABSOLUTELY NO WARRANTY;
This is free software, and you are welcome to redistribute and/or modify
it under the conditions outlined in the terms of the GNU General Public Licenses
as published by the Free Software Foundation either version 3 or later.
GNU General Public License version 3 is provided with this program as LICENSE.txt

SummonChimera version 1.0 by Joshua Patrick Katz 

CONTENTS:
	bin/SummonChimera.pl: Perl script used to find viral integrations in NGS alignment data
	lib/Chimera.pm: Perl object used by SummonChimera
	LICENSE.txt: contains version 3 of the GNU General Public License
	README: this file

PREREQS:
	While SummonChimera does not require any non-core Perl module in order to run, input files are
	generated by external programs. BLAST can be found at ftp://ftp.ncbi.nlm.nih.gov/blast/. Any
	mapping program which generates SAM files can be used though Bowtie2 and BWA are the two
	which were tested: 
	Bowtie2: http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.1.0/ 
	BWA: http://sourceforge.net/projects/bio-bwa/files/

BASH INSTALLATION:
	Add lib to your PERL5LIB enviroment variable
	Add bin to your PATH enviroment variable
	Replace Perl shebang line in SummonChimera.pl with results from `which perl`

TESTING:
	Run the following command:
		perl TestSummonChimera.pl
	SummonChimera is properly installed if the output of TestSummonChimera is: 
		No errors encountered when running SummonChimera.pl

DEVELOPMENT:
	Currently SummonChimera predicts integrations as if the virus genome is circular. When using
	linear genome viruses incorrect predictions may be made. This will soon be rectified.

USAGE:
	This pipeline is an example and is not the fastest method.
	INPUT:
		one.fq - file continaing first read in paired-end sequencing
		two.fq - file containing second read in paired-end sequencing
		host.fa - file containing host genome
		virus.fa - file containing virus genome
		virusID - the fasta identifier found in virus.fa
	SCRIPT:
		bowtie2-build host.fa,virus.fa host-virus.bowtieDB
		bowtie2 -x host-virus.bowtieDB -1 one.fq -2 two.fq 1> virus-host.sam
		#add samtools / perl one liner to retrieve unmapped
		makeblastdb -in host.fa -dbtype nucl -out host.blastDB
		makeblastdb -in virus.fa -dbtype nucl -out virus.blastDB
		blastn -db virus.blastDB -query unmapped.fa -word_size 16 -outfmt 6 1> virus-host.blastn.txt
		blastn -db host.blastDB -query unmapped.fa -word_size 16 -outfmt 6 1>> virus-host.blastn.txt
		SummonChimera.pl -b virus-host.blastn.txt -s virus-host.sam -v virudID > Integrations.tsv