Dragmap

Dragmap is the Dragen mapper/aligner Open Source Software.

Installation

Using bioconda

Dragmap is available in the Bioconda package manager.If you choose to install with bioconda, please first follow the bioconda install procedure from here: https://bioconda.github.io/user/install.html

Once 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++17 compatible compiler (e.g gcc-c++ >= 7.1)
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

Pull requests

We are not accepting pull requests into this repository at this time, in particular because of conflicts concerns with our internal repository. For any bug report / recommendation / feature request, please open an issue.

AntonioGPS/DRAGMAP