Dragmap is the Dragen mapper/aligner Open Source Software.
Dragmap is available in the Bioconda package manager. If you have bioconda installed, you should be able to install Dragmap with conda install dragmap
(or conda create -n myenv dragmap
to install in a new environment). This will install the dragen-os
binary.
Compilation was tested on CentOS 7
- C++11 compatible compiler (e.g gcc-c++ >= 4.8.5-36.el7_6.2)
- GNU make >= 3.82
- Boost library : boost169-devel >= 1.69.0-1.el7
- For unit tests : googletest (>= v1.6)
- Hardware: x86_86, 64GB RAM minimum
- OS: Centos >= 7.7
The basic procedure is
make
Binary will be generated in ./build/release/
Then optionally, to install to /usr/bin/
make install
By default make will compile and launch unit tests. To disable unit tests, use HAS_GTEST=0, e.g. :
HAS_GTEST=0 make
To compile with unit tests, if google test was installed in user space, it might be required to set GTEST_ROOT and LD_LIBRARY_PATH to where gtest was installed, e.g. :
export GTEST_ROOT=/home/username/lib/gtest
export LD_LIBRARY_PATH=/home/username/lib/gtest/lib
- GCC_BASE
- CXX
- BOOST_ROOT
- BOOST_INCLUDEDIR
- BOOST_LIBRARYDIR
dragen-os --help
dragen-os --build-hash-table true --ht-reference reference.fasta --output-directory /home/data/reference/
dragen-os --build-hash-table true --ht-reference hg38.fa --output-directory /home/data/reference/ --output-file-prefix=dragmap.hg38_alt_masked --ht-mask-bed=fasta_mask/hg38_alt_mask.bed
Output result to standard output
dragen-os -r /home/data/reference/ -1 reads_1.fastq.gz -2 reads_2.fastq.gz > result.sam
Or directly to a file :
dragen-os -r /home/data/reference/ -1 reads_1.fastq.gz -2 reads_2.fastq.gz --output-directory /home/data/ --output-file-prefix result
dragen-os -r /home/data/reference/ -1 reads_1.fastq.gz > result.sam