datasnu / dude-seq

DUDE-Seq: Fast, flexible, and robust denoising of nucleotide sequences

HOW TO INSTALL

$ make && make install

DEPENDENCIES

[REQUIRED DEPENDENCIES] The required dependencies are: 1)libboost-dev, 2) libgsl0-dev, 3) liblapack-dev, 4) zlib1g-dev To install the dependencies, type the following command:

$ sudo apt-get install libboost-dev libgsl0-dev liblapack-dev zlib1g-dev

[OPTIONAL DEPENDENCIES] The python dependencies are: 1) biom-format, 2) cogent, 3) numpy, 4) qcli To install the dependencies, type the following command:

$ sudo pip install biom-format cogent numpy qcli

INPUTS

The example formats of the inputs are in Example directory. e.g., Artificial.fasta, Artificial.dat

HOW TO MAKE DAT_FILE

The following command makes DAT_FILE from SFF_FILE:

$ Scripts/process_sff.py -f -i [SFF_FILE]

EXAMPLE

'DUDE-Seq-1.sh' do DUDE-Seq-1 algorithm.

$ DUDE-Seq-1.sh [FASTA_FILE]

'DUDE-Seq-all.sh' do DUDE-Seq-2 then DUDE-Seq-1 algorithm.

$ DUDE-Seq-all.sh [DAT_FILE]