Dragmap

This is a fork prividing Dragmap binary file and docker/singularity image.

Dragmap is the Dragen mapper/aligner Open Source Software.

You can download the binary file in release, it should work on any debian based distro. Otherwise a straightforward approach is to utilize the pre-built Docker/Singularity image I've created.

Install with Singularity or Docker

This image also incorporates some useful tools such as bcftools, samtools, tabix, sambamba, bedtools, mosdepth and bbmap for added convenience. To install the DragMap Docker/Singularity image, run the following commands:

# 1. Install with Singularity and test it
singularity pull docker://gambalab/dragmap

singularity exec --bind /usr/lib/locale/ \
    /path/to/dragmap_latest.sif \
    dragen-os --help

# 2. Install with Docker and test it
docker pull gambalab/dragmap

docker run -u $(id -u):$(id -g) \
    gambalab/dragmap dragen-os --help

Below is an example of how to use the image with Singularity. The Docker usage is similar, requiring only the appropriate mounting of input files using the -v argument.

# Let's define e DRAGMAP_exec variable to excec the several commands 
DRAGMAP_exec="singularity exec --bind /usr/lib/locale/ path/to/dragmap_latest.sif"

# Build hash table of a reference fasta file
${DRAGMAP_exec} dragen-os \
    --build-hash-table true \
    --ht-reference reference.fasta \
    --output-directory ${ref_genome_dragmap}

# Align paired-end reads
${DRAGMAP_exec} dragen-os \
    --preserve-map-align-order true \
    --num-threads ${cpus} \
    --RGID "${ID}" \
    --RGSM "${sample}" \
    --ref-dir ${ref_genome_dragmap} \
    --fastq-file1 ${fastqR1} --fastq-file2 ${fastqR2} | \
     ${DRAGMAP_exec} samtools view --threads 2 -bh -o ${BAM_OUT}

ALN PIPELINE

In the docker/singularity image there is also a one click pipeline we built. It starts from fastQ files and can evantually trim it before to alignment. It also removes dup reads using samtools markdup.

# Let's define e DRAGMAP_exec variable to excec the several commands 
DRAGMAP_exec="singularity exec --bind /usr/lib/locale/ path/to/dragmap_latest.sif"

# Let's see the help
${DRAGMAP_exec} run_aln.sh -h

This pipeline employs DragMap for efficient read alignment, incorporating optional preprocessing and post-processing steps.

Key Steps:

  1. Optional Trimming: If enabled, reads are initially trimmed using the BBduk tool to remove low-quality bases and adaptors.
  2. Alignment: The trimmed or original reads are aligned to the reference genome using DragMap.
  3. Duplicate Marking and Removal: Samtools markdup is utilized to identify and remove potential PCR duplicates from the aligned reads.
  4. Output Organization: Results are organized into three distinct folders:
	 4.1 aln: Contains the final aligned BAM file.
	 4.2 fastq: Stores the trimmed FASTQ files if trimming was performed.
	 4.3 stat: Provides statistical information about trimming (if applicable) and alignment coverage.

This streamlined workflow ensures accurate and efficient read alignment, while the organized output facilitates downstream analysis.

Syntax: run_dragen.sh [h|s|1|2|o|r|c|t|b|d]
options:
-h     Print this Help.
-c     Number of cpus to use. (Required)
-o     Output directory. (Required)
-s     Sample name. (Required)
-1     Path to the read1 FASTQ. (Required)
-2     Path to the read2 FASTQ. (Required)
-r     Path to the Dragmap reference folder. (Required)
-t     Trimming. Default false. (Optional)
-b     BED file with regions will be used to compute coverage. Otherwise coverage stats are computed whole genome. (Optional)
-d     Delete trimmed fastQ. Default false. (Optional)

So a typical case of use will be something like this:

${DRAGMAP_exec} \
    run_aln.sh \
   -c 24 \
   -o /path/to/output_folder \
   -s ${SAMPLE} \
   -1 /path/to/fastQ_R1 \
   -2 /path/to/fastQ_R2 \
   -r /path/to/dragmap_idx_folder \
   -t "true"

At the end of alignmet output files are stored under /path/to/output_folder/${SAMPLE}

Build from source a standalone dragen-os file

Install

The basic procedure is

export HAS_GTEST=0
export STATIC=1
make -j 4

Binary will be generated in ./build/release/

Then optionally, to install to /usr/bin/

make install

Acknowledgements

Our singularity container happily makes use of many open source packages. We would like to specifically call out a few key ones:

• bcftools
• samtools
• tabix
• sambamba
• bbmap
• dragen-os
• bedtools
• mosdepth

We thank all of the developers and contributors to these packages for their work.