AmpliMap is a bioinformatic pipeline for aligning amplicon reads to a DNA database. This pipeline is based on Nextflow.
git clone https://github.com/chaoatic/amplimap-nf.git
cd amplimap-nf
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]
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
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.
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