Sanibel

What to do

The Nextflow pipeline is used to analyze NGS data in fastq format from the bacterial genome. It is a Nextflow version of the Flaq_amr pipeline (FL-BPHL's standard bacterial assembly pipeline with AMR detection). Compared with Flaq_amr, Sanibel significantly reduces runtime and is especially suitable for analysis of large sample sizes. In addition, some additional analyses of Neisseria, H.influenzae, Legionella, Shigella, group A strep, Klebsiella, Salmonella, E.coli, and plasmid are added, such as identifying clonal complex and serotype of Neisseria and H.influenzae species.

Prerequisites

Nextflow is needed. The details of installation can be found at https://github.com/nextflow-io/nextflow.

Python3 is needed. The package "pandas" should be installed by pip3 install pandas if not included in your python3.

Singularity/APPTAINER is needed. The details of installation can be found in https://singularity-tutorial.github.io/01-installation/.

SLURM is needed.

Recommended conda environment installation

conda create -n SANIBEL -c conda-forge python=3.10 pandas

conda activate SANIBEL

How to run

Option1, your data file names directly come from Illumina output:

1. put your data files into the directory /fastqs. Your data file's name should look like "XZA22002292-XS-ASX550430-220701_S143_L001_R1_001.fastq.gz".
2. open the file "params.yaml", and set the two parameters absolute paths. They should be ".../.../fastqs" and ".../.../output".
3. get to the top directory of the pipeline, run

sbatch ./sanibel_illumina.sh

Option2, your data file names do not directly come from Illumina output:

1. put your data files into the directory /fastqs. Your data file's name should look like "XZA22002292_1.fastq.gz", "XZA22002292_2.fastq.gz"
2. open the file "params.yaml", and set the two parameters absolute paths. They should be ".../.../fastqs" and ".../.../output".
3. get into the directory of the pipeline, run

sbatch ./sanibel.sh

By Docker

By default, the pipeline uses singularity to run containers and is wrapped by SLURM. If you want to use docker to run the containers, you should use the command below: If your data file names do not directly come from Illumina output,

sbatch ./sanibel_docker.sh

If your data file names directly come from Illumina output,

sbatch ./sanibel_illumina_docker.sh

Version updates

https://github.com/BPHL-Molecular/Sanibel.wiki.git

Note1: some sample data files can be found in the directory /fastqs/sample_data. If you want to use these data for the pipeline test, please copy them to the directory /fastqs.

Note2: If you want to get email notification when the pipeline running ends, please input your email address in the line "#SBATCH --mail-user=" in the batch file that you will run (namely, sanibel.sh, sanibel_illumina.sh, sanibel_docker.sh, or sanibel_illumina_docker.sh).