Daytona_Pb

A pipeline is used to analyze SARS-CoV-2 sequencing data from PacBio equipment.

What to do

The pipeline can analyze SARS-CoV-2 sequencing data from PacBio equipment. The sample's sequencing quality, mapping/alignment with reference, coverage, SNPs, annotation, consensus sequence, lineage, phylogeny, etc can be analyzed.

Prerequisites

Nextflow should be installed. The detail of installation can be found in https://github.com/nextflow-io/nextflow.

Python3 is needed.

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

PacBio SMRTLINK stand-alone tools (lima, mimux, pbindex, pbmm2, VCFCons) are needed. About how to install them, please see the file "How_to_install_smrtlink_tools.txt".

Before running

1. Add the reads file in bam format (*.bam) from PacBio equipment to the folder "hifireads"
2. Add the file of M13 barcodes in fasta (*.fasta) format to the folder "M13barcodes".
3. Add enrichment probes file in fasta format (*.fasta) to the folder "enrichment_probes".
4. Add biosample sheet file in csv format (*.csv) to the folder "biosample_sheet". Only two columns are allowed in the sheet. One column is barcode name, the other column is sample name. A sample sheet can be found in the folder "biosample_sheet".

How to run

1. open file "parames.yaml", set the full paths to the folders of input, probe, output, and reference.
2. get into the top of the pipeline directory, then run

./daytonapb.sh

If SLURM is used, you can run

sbatch ./daytonapb.sh

Results

All results can be found in the directory /output.