README

To run Alignment code:
NOTE: This code was compiled on a Windows machine.
1. Download Alignment.zip from github repository: https://github.com/AyushiSinha/BDSLSS/tree/fb202810dd7f1cafbcba28ff8fa23216b89a6a0d
2. Extract all files
3. In Alignment/Release/:
	a. Alignment.exe is the executable
	b. Input Reference:
		(Short) lambda_virus_short.fa
		(Long) lambda_virus.fa
	c. Input Reads:
		(Short) reads.fq
		(Long) reads_1.fq
	d. Output Files:
		SAM: Alignments in the regular SAM output format
		GL: Sorted alignments in a format suitable as input for GraphLab.
4. To run
	a. Quick run (1 second): Alignment.exe --ref lambda_virus.fa --read reads.fq --out out_lambda_virus_short
	b. Slow run (2 minutes): Alignment.exe --ref lambda_virus.fa --read reads_1.fq --out out_lambda_virus

NOTE: A Linux/Mac version of this code will be available soon!


#####################################################################


To run Assembly code:
NOTE: This code is on the damsl.cs.jhu.edu cluster, node qp5.
1. In /home/shuya/graphlab/release/apps/assembly/
	a. Input: 
		(Short) GraphLab_Input.txt
		(Long) out_lambda_virus.GL
	b. Output
		result: contains the resequenced genome (also available on the github repository)
	c. Makefile: CMakeLists.txt
2. To run
	a. Type: make
	b. Quick run (1 second): ./assmbly --infile=GraphLab_Input.txt --outfile=output --source=33 --destination=5
	c. Slow run (4 hours): ./assmbly --infile=out_lambda_virus.GL --outfile=output --source=3903 --destination=7215

			OR

In case you are running on a different cluster:

1. Download and install GraphLab. Here is how to install GraphLab on Linux: http://graphlab.org/tutorials-2/graphlab-installation-on-ubuntu/
2. After installation, create a folder named 'assembly' under graphlab/apps, download assembly_final.cpp and Makefile from gitbub repository given above.
3. Put assmebly_final.cpp and CMakeList.txt under graphlab/apps/assembly
4. In graphlab/, type ./configure
5. Then create a folder named 'assembly' under graphlab/release/apps.
6. Put GraphLab_Input.txt and out_lambda_virus.GL under graphlab/realease/apps/assembly.
7. In graphlab/realease/apps/assembly, type:
	a. make
	b. Quick run (1 second): ./assmbly --infile=GraphLab_Input.txt --outfile=output --source=33 --destination=5
	c. Slow run (4 hours): ./assmbly --infile=out_lambda_virus.GL --outfile=output --source=3909 --destination=7215

NOTE: You need to specify (manually enter) the id for source and destination (first and last read IDs from the input file)