1. Run blast on reads. Output format should be specified with -outfmt 6. The details about this format can be found here. https://sites.google.com/site/wiki4metagenomics/tools/blast/blastn-output-format-6
	
	blastn  -query genes.fasta  -subject genome.fasta  -outfmt 6

Additional notes:
	
	Blast is an alignment software that finds alignments for sequences in a query file with sequences in a reference file. 
	How to install and run blast alignment: https://doctorlib.info/medical/blast/11.html


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2. Analyze the blast output

	compile analyse_blast_csvout.cpp:
	
	g++ analyse_blast_csvout.cpp -o abcout.exe

	Analyze:

	./abcout.exe <blast_output_file> <amr_file> <output_filename> <E_value_threshold> <output_filename.csv>

Additional notes:
	
	E-value output by blast is in exponential notation ex 2.44e-12. The figure after the '-' gives the exponent figure which is used to determine if an alignment is above the E_value_threshold. Higher the exponent figure, better the alignment.
	More on E value: http://www.metagenomics.wiki/tools/blast/evalue
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3. Find unique query genes/reads found in a blast output file

	compile unique_genes.cpp:

	g++ unique_genes.cpp -o unique_genes.exe

	Run:
	
	/unique_genes.exe <blast_output_file> <output_filename>