tCANS: Consensus calling for (Tiling) Amplicon Nanopore Sequencing

Description

tCANS is a Nextflow pipeline designed to generate a single contiguous consensus sequence from tiling amplicon Nanopore sequencing data. The pipeline uses samtools ampliconclip, iVar and medaka to perform primer trimming, consensus calling and consensus polishing, respectively.

Installation

# Install Pre-requisites
 - Nextflow >= v21.0.0
 - Conda or Docker

# Download workflow locally
nextflow pull -r main jimmyliu1326/tCANS

# Check if the pipeline was successfully installed
# by printing the pipeline help message
nextflow run -r main -latest jimmyliu1326/tCANS --help

Pipeline usage

Docker (Default)

nextflow run -r main -latest jimmyliu1326/tCANS --input samples.csv --out_dir /path/to/output -profile docker

Singularity

nextflow run -r main -latest jimmyliu1326/tCANS --input samples.csv --out_dir /path/to/output -profile singularity

Singularity + Slurm

nextflow run -r main -latest jimmyliu1326/tCANS --input samples.csv --out_dir /path/to/output -profile slurm,singularity --account [slurm_account]

Below is the complete list of pipeline options available:

Required arguments:
    --input                       Path to .csv containing two columns encoding Sample ID and path to raw reads DIRECTORY
    --primers                     Path to .bed encoding the position of each primer
    --reference                   Path to .fasta reference sequence that corresponds to the coordinates in the primers .bed file
    --out_dir                      Output directory path
Optional arguments:
    --host                        Path to host reference genome in FASTA format for dehosting raw reads
    --notrim                      Disable adapter trimming by Porechop
    --gpu                         Accelerate specific processes that utilize GPU computing. Must have NVIDIA Container
                                  Toolkit installed to enable GPU computing, otherwise use CPU. (Only works with -profile docker)
    --help                        Print pipeline usage statement

Input file formats

To understand the required file formats for the arguments --input and --primers, take a look at the example files located under example/ in the repo.