#pcluster#
Parallel hierarchical single-linkage clustering for DNA sequences. Input reading and verification, K-mer comparison, sequence alignment
with SIMD, and some small utility methods were using the code from swarm with some modifications
within these classes: db, cpu_info, util, qgram, search8, search16, and scan.
##Compiling## To compile executable "main" for general usage (debug log disabled) use:
make clean main
To compile executable "test" for testing (debug log enabled and results are sort alphabetically by header) use:
make clean test
To compile both version use:
make clean all
##Unit Test##
To run short test, execute test.sh
To run full test (with valgrind), execute run.sh
The unit test compares the result from pcluster with the result from swarm that are both sorted alphabetically by header. They
are expected to be exactly the same.
##Run:##
./main -t[threadcount] -z filename.fas
Add this option -y=[depth] to enable economic search (skipping comparisons based on triangle inequality).
Depth is the level of connections that will be using the skipping scheme. To skip only first level of connections use -y=2, while to skip up to sixth level of connections use -y=7.
Based on our experiment input with short sequences (less than or equal to 125 nucleotides in average) do not benefit from multiple level connections when running clustering for d>1. Instead, the first level setting -y=2 is advised to use for this type of short sequence input.
The program will run as brute force (comparing all possible combinations) when option -y is not specified, or if it is set as -y=1.
Other options for this program:
-d, --differences INTEGERresolution (default 1)-h, --helpdisplay this help and exit-o, --output-file FILENAMEoutput result filename (default isresult.log)-t, --threads INTEGERnumber of threads to use (default 1)-m, --match-reward INTEGERreward for nucleotide match (default 5)-p, --mismatch-penalty INTEGERpenalty for nucleotide mismatch (default 4)-g, --gap-opening-penalty INTEGERgap open penalty (default 12)-e, --gap-extension-penalty INTEGERgap extension penalty (default 4)-y, --depth INTEGERmaximum level for economic search, as explained before
##Some notes about preparing fasta file:## Same as in swarm, fasta file needs to be sorted decreasing by abundance and marked with abundance information, e.g.
>sequence-header_12345