MPI should be installed in the system before compiling.

Configure the AltMakefile with correct paths for boost and sparsehash

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Compile

for distributor tool

make -f AltMakefile kmer_distributor

for counting tool

make -f AltMakefile kmer_counter

for query tool

make -f AltMakefile finalizer

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Run

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for distributor tool

mpirun <mpi args> ./kmer_distributor.out <data file> <output folder>

example

mpirun -np 16 --hostfile hosts.txt ./kmer_distributor.out vesca.fastq /home/user1/tempfolder/

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for counting tool

mpirun <mpi args> ./kmer_counter.out <encoded file> <k> <output folder>

example

mpirun -np 16 --hostfile hosts.txt ./kmer_counter.out /home/user1/tempfolder/encoded.bin 28 /home/user1/tempfolder/

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for querying tool

mpirun <mpi args> ./finalizer.out <k> <query file> <no of queries> <output folder>

example

mpirun -np 16 --hostfile hosts.txt ./finalizer.out 28 query.txt 10 /home/user1/tempfolder/

Example format of query kmer file (for k=5)

AAAAA
AAAAC
ACGTT
AAAAT
TTTTG
TTTTT

For example if no of queries = 4, then only the first 4 kmers will be queried for count.

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