amplimap-nf

AmpliMap is a bioinformatic pipeline for aligning amplicon reads to a DNA database. This pipeline is based on Nextflow.

Getting started

Prerequisites

• Nextflow
• Miniconda or Mamba

Installation

git clone https://github.com/chaoatic/amplimap-nf.git
cd amplimap-nf

Usage

Usage: nextflow run amplimap.nf [OPTION...]

Mandatory arguments:
    --data_dir      Path to sequences directory with sequences in fastq.gz format
    --db            Path to database file with sequences in fasta format
    --result_dir    Path to directory containing results

Optional arguments:
    --min_length    Minimum length (bp) for a read to be retained
                    [Default: 1]
    --max_length    Maximum length (bp) for a read to be retained
                    [Default: 2147483647]
    --min_qscore    Minimum average PHRED score for a read to be retained
                    [Default: 1]
    --threads       Number of parallel threads to use
                    [Default: 4]

Example usage

nextflow run amplimap.nf \
    --data_dir "/DATA/DIRECTORY" \
    --db DB.fasta \
    --result_dir "/RESULT/DIRECTORY" \
    --min_length 500 \
    --max_length 1000 \
    --min_qscore 10 \
    --threads 4

Overview

This pipeline is composed of a set of processes to compare amplicon reads against a reference database, then produce a coverage report for each sample.

• concatenateFastq: import all fastq files and concatenate them together into each barcode.
• rawSequenceVisualization: produce graphs and data visualizations of raw read sequences for each barcode.
• filterFastq: filter reads according to parameters provided.
• filterSequenceVisualization: produce graphs and data visualizations of filtered read sequences.
• generateSequenceReport: generate statistic report of each barcode sequence.
• generateCoverageReport generate coverage report of each barcode sequence.

Citation

If you use AmpliMap please cite:

• Wouter De Coster, Rosa Rademakers, NanoPack2: population-scale evaluation of long-read sequencing data, Bioinformatics, Volume 39, Issue 5, May 2023, btad311, https://doi.org/10.1093/bioinformatics/btad311
• Heng Li, Minimap2: pairwise alignment for nucleotide sequences, Bioinformatics, Volume 34, Issue 18, September 2018, Pages 3094–3100, https://doi.org/10.1093/bioinformatics/bty191
• Shen W, Le S, Li Y, Hu F (2016) SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation. PLOS ONE 11(10): e0163962. https://doi.org/10.1371/journal.pone.0163962
• Twelve years of SAMtools and BCFtools Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A McCarthy, Robert M Davies, Heng Li GigaScience, Volume 10, Issue 2, February 2021, giab008, https://doi.org/10.1093/gigascience/giab008