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SeqOthello

#README for SeqOthello SeqOthello supports fast coverage query and containment query. ##Compile SeqOthello is tested on linux platform with the following system settings. The performance is optimized for Intel CPUs with SSE4.2 support.

cmake >= 2.8.4
gcc >= 4.9.1
libz >= 1.2.3

To compile the SeqOthello tool chain, decompress the source code and execute the following commands in the source folder.

./compile.sh

Then you can find the compile resutls in the build/bin folder.

##Build To build the SeqOthello structure, please first prepare the Jellyfish-generated Kmer files. For test purpose, please use the following command to generate a toy set of Kmers in the kmer folder, and then we will build SeqOthello from it.

./genExample.sh

There are three steps in building SeqOthello: 1. Convert the Kmer files to binary files. 2. Group them together. 3. Execute the Build program. You can simply prepare the commands using the wrapper. Simply execute the tool to generate the scripts to build the SeqOthello map, by

./genBuildFromJellyfishKmers.sh

For all prompted input questions, just press Enter to use the default value for the example data set. Then three scripts will be generated and you can execute them.

./ConvertToBinary.sh
./MakeGroup.sh
./BuildSeqOthello.sh

And the generated SeqOthello file can be found in out folder.

###Prepare the kmers in parallel Each line of the generated scripts contains a command to prepare the files. The commands in each of the generated scripts can be executed in parallel. For example, with GNU Parallel, you can run

cat ConvertToBinary.sh | parallel

##Query

Containment Query

build/bin/Query --map-folder=out/ --transcript=test.fa --output=queryresult --lthread=16 --qthread=16> querylog

Coverage Query

build/bin/Query --map-folder=out/ --transcript=test.fa --detail --output=queryresult --lthread=16 > querylog

##OnlineQuery Use the following command to start a server on the machine, (e.g., on TCP port 3322). The service will run as a deamon.

build/bin/Query --map-folder=out/ --start-server-port 3322

In another terminal, run the Client program. build/bin/Client --transcript=kmer/test.fa --coverage --output=result --port=3333