The Nanopore Genome Assembly Pipeline (NanoGAP) utilises a variety of open-source tools and software to automate a non-hybrid (long reads only) genome assembly and self-correction of error prone nanopore reads

• Developed specifically for bacterial genomes.
• Requires raw/uncorrected Oxford Nanopore Technologies (ONT) long reads only (.fastq).
• Assembly of unknown isolates (no predicted genome size needed).
• Identify nearest bacterial organism.

Conda is required for installation. You can download and install conda for Linux here.

NanoGAP uses a number of open source projects:

• flye
• medaka
• barrnap
• blast

git clone https://github.com/escasinas/nanogap.git
cd nanogap
source install.sh

Input

• A single .fastq file.

or

• A directory containing multiple .fastq files.

Output

• Genome assembly in .fasta format.
• BLAST output of the genome's 16S rRNA.
• CSV output containing assembly information.

Command

For a single fastq file

conda activate nanogap
python nanogap.py path/to/file.fastq [options]

For a directory containing fastq files

conda activate nanogap
python nanogap.py path/to/reads_directory [options]

-h | --help Show help message and exit.

-t | --threads Number of threads/CPUs to run Minimap2, Flye, Racon, Medaka and Barrnap (default: MAX CPU).

-o | --outdir Name of output directory (default: ngap_output).

-m | --model Medaka model. Please see the Medaka repo for more information (default: r941_min_high_g360).