Dragmap

Dragmap is the Dragen mapper/aligner Open Source Software.

Installation

Using bioconda

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.

Build from source

Prerequisites

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

Install

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

Other variables controlling the build process:

GCC_BASE
CXX
BOOST_ROOT
BOOST_INCLUDEDIR
BOOST_LIBRARYDIR

Basic command line usage

Command line options

dragen-os --help

Build hash table of a reference fasta file

dragen-os --build-hash-table true --ht-reference reference.fasta  --output-directory /home/data/reference/

Build hash table using an alt-masked bed file

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

Align paired-end reads :

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

Align single-end reads :

dragen-os -r /home/data/reference/ -1 reads_1.fastq.gz  >  result.sam

loreseeker/DRAGMAP