runAssembly

Packaging Newbler with a singularity container enables de novo assembly in any Linux environment.

Requirement

Install system dependencies

You must first install development tools and libraries to your host.

On Debian-based systems, including Ubuntu:

# Ensure repositories are up-to-date
sudo apt-get update
# Install debian packages for dependencies
sudo apt-get install -y \
    build-essential \
    libseccomp-dev \
    pkg-config \
    squashfs-tools \
    cryptsetup \
    curl wget git

On CentOS/RHEL:

# Install basic tools for compiling
sudo yum groupinstall -y 'Development Tools'
# Ensure EPEL repository is available
sudo yum install -y epel-release
# Install RPM packages for dependencies
sudo yum install -y \
    libseccomp-devel \
    squashfs-tools \
    cryptsetup \
    wget git

Download & install Go Language

Singularity is written in Go language, and may require a newer version of Go than is available in the repositories of your distribution. We recommend installing the latest version of Go from the official binaries.

wget https://go.dev/dl/go1.14.12.linux-amd64.tar.gz
tar -C /pub/software -xzvf go1.14.12.linux-amd64.tar.gz
rm go1.14.12.linux-amd64.tar.gz
echo 'export PATH=/pub/software/go/bin:$PATH' >> /etc/profile.d/env.sh
source /etc/profile.d/env.sh

Download & install Singularity

You can configure, build, and install Singularity using the following commands:

wget https://github.com/hpcng/singularity/releases/download/v3.7.2/singularity-3.7.2.tar.gz
tar -xzf singularity-3.7.2.tar.gz
cd singularity
./mconfig
cd builddir
make
sudo make install

And that's it! Now you can check your Singularity version by running:

singularity --version

If you wish to use singularity in any path, we recommend adding singularity to the PATH environment variable.

De novo assembly with runAssembly.sif

singularity exec runAssembly.sif runAssembly

If the following prompt appears, the installation is successful.

Error in runAssembly: No read data files are specified.
Usage: runAssembly [-o projdir] [-nrm] [-p (sfffile | [regionlist:]analysisDir)]... (sfffile | [regionlist:]analysisDir)...

singularity exec runAssembly.sif runAssembly -cpu 10 -het -sio -m -urt -large -s 100 -nobig -o $output_dir Hifi.cut20k.fa
# -het: Flag to enable Heterozygotic mode, which causes the assembler to choose a path between 2 contigs when there is ambiguity regarding the path that should be taken.
#       By default, the assembler will not choose a path when ambiguity exists
# -sio: Flag to invoke serial I/O. Use for projects with > 4 million reads.
# -m: Keeps sequence data in memory Increases speed
# -urt: Extend contigs using the ends (tips) of single reads
# -large: Speeds up assembly but reduces accuracy
# -nobig: Skip output of large files (.ace, 454AlignmentInfo.tsv) Default: no
# -o <output-directory>