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cd BFCounterForStrobemers
make
cd ..

cd SAKEandSPOA/spoa
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=Release ..
make
cd ../../..

cd SAKEandSPOA/sake
make sake
cd ../..

./BFCounterForStrobemers/BFCounter count -n <int> -m <int> -l <int> -k <int> -w <int> -f <int> -t <int> -o <string> reads.fastq

Where:
n = approximate number of output strobemers (check the original BFCounter documentation)
m = number of minimizers
l = minimizer length
k = strobemer length (m*l)
w = minimizer window length
f = distance between two consecutive minimizer windows
t = number of threads
o = file path for the output strobemers (binary format)
reads.fastq is just the input read set file (fastq format)

./BFCounterForStrobemers/BFCounter dump -k <int> -i <string> -o <string>

Where:
k = strobemer length
i = input binary file path (output from the previous step)
o = output file path for the readable strobemers

./SAKEandSPOA/sake/sake -k <string> -r <string> -o <string> -n <int> -l <int> -s <int> -f <int> -b <float> -z <float> -a <int> -g <int> -c <int> -t <int>

Where:
k = path to the file with readable strobemers (output from previous step)
r = path to the read set file (fastq format)
o = path to the output file where consensus sequences are written
n = number of minimizers in the strobemers
l = length of the minimizers in the strobemers
s = minimizer window size
f = distance between two consecutive minimizer windows
b = bundling threshold
z = relative bundle support threshold
a = minimum strobemer abundance
g = hard bundle support threshold
c = character support threshold
t = number of threads

python ./pytools/split_into_kmers.py <string1> <string2> <int>

Where:
The first string is the path to the file with the consensus sequences
The second string is the path to the output file where the k-mers are written
And the integer is the length of the k-mers

python ./pytools/kmer_orienter.py <string1> <string2> <int1> <int2>

Where:
The first string is the path to the file with the k-mers
The second string is the path to the file where oriented k-mers are written
The first integer is the strobemer length
The second integer is an abundance threshold that should be set to 1 (This parameter does not make much sense anymore, it is due to leftover code from previous version of the script. Should be fixed at some point in the future.)

sort <string1> > <string2> 
uniq <string2> > <string3>

Where:
String 1 is path to the file with oriented k-mers.
String 2 is path to the file where sorted and oriented k-mers are written.
String 3 is path to the file where unique sorted and oriented k-mers are written. [This is the final output file.]