CELIA: automatiC gEnome assembLy marIne prokAryotes

Introduction

CELIA is a bioinformatics workflow used to automate the genome assemblies of prokaryotes from Illumina data

For now, the workflow allows:

to make a quality control of the data using FastQC and MultiQC
to assemble the genome using Unicycler
to remove contaminants (vectors, adpatators or PhiX) using NCBI UniVec database and python script developped by the SeBiMER
to evaluate the assembly quality using BUSCO and the mapping coverage (Bowtie2 + MoseDepth)
to compute ANI scores using dedicated database (FastANI)
to make a structural annotation (Prokka)
to search for antibiotics and secondary metabolite (AntiSMASH)

Dependencies

Nextflow >= 20.04.x
Singularity or Docker

Quick start

Clone the current gitlab repertory in your working directory

git clone https://gitlab.ifremer.fr/bioinfo/celia.git

Add a directory with your data (paired fastq.gz files)

celia/
...
└── test_data
    ├── 1629_S50_L001_R1.fastq.gz
    ├── 1629_S50_L001_R2.fastq.gz
    ├── AMNU_S04_L001_R1.fastq.gz
    ├── AMNU_S04_L001_R2.fastq.gz
    ├── RTFM_S25_L001_R1.fastq.gz
    └── RTFM_S25_L001_R2.fastq.gz

Set the configuration file

vim conf/custom.conf

Run the analysis

nextflow run main.nf -profile custom,singularity

Examples

1 - Run using Singularity on a local computer/server

nextflow run main.nf -profile custom,singularity --projectName run-test --rawdata_dir "test_data/*_R{1,2}.fastq.gz"

2 - Same with HPC configuration

nextflow run main.nf -profile custom,singularity -c /appli/bioinfo/hpc/nextflow/ifremer.config

3 - Restart a run partially failed

nextflow run main.nf -resume -profile custom,docker -c /appli/bioinfo/hpc/nextflow/ifremer.config

Workflow process

License and Credits

CELIA is released under the GNU Affero General Public License, Version 3.0. AGPL

It is developped by Alexandre Cormier, bioinformatics engineer at the bioinformatics service of IFREMER (SeBiMER).