Requirements
SEECER requires the following libraries/programs:
- GNU Scientific Library
- SeqAn
- JELLYFISH
- OPENMP API
Download
SEECER 0.1.3 is available (bundled with SeqAn and JELLYFISH 1.1.11) here: SEECER-0.1.3.tar.gz. The source code is also hosted at GitHub.
Installation
GNU Scientific Library
apt-get install gsl
or
port install gsl
(MacPorts on Mac OSX).
SeQan
The required files are bundled with SEECER's distribution. You can also download the library on your own here.
JELLYFISH
The source codes are bundled with SEECER's distribution. You can also download the library on your own here. To compile:
./configure && make
SEECER
./configure && make
Running a simple data set
We include a small data set, to run on this
paired-end data set:
mkdir tmp && bash ./bin/run_seecer.sh -t
tmp testdata/SRR027877-small-p1.fastq testdata/SRR027877-small-p2.fastq
More details are available in the Manual.