AmpliGone

AmpliGone is a tool which accurately finds and removes primer sequences from NGS reads in an amplicon experiment.

In contrast to a lot of other primer-removal tools, AmpliGone does not actively look for primer sequences within the NGS reads. Instead, reads are trimmed based on primer sequence coordinates in relation to a given reference sequence. Additionally, AmpliGone is able to compensate for, and therefore properly clean, reads that start or end outside of a primer-region as this is a common occurrence in amplicon-based sequencing data.

AmpliGone is build and tested with Nanopore and Illumina data (fastq) in mind and supports ‘end-to-end’, ‘end-to-mid’ and ‘fragmented’ amplicons to be cleaned.
Please see this page to learn more about this terminology.

Installation instructions

AmpliGone can be installed easily with conda or pip. Installation through conda is recommended.

Installation with conda

conda install -c bioconda ampligone

Installation with pip

pip install AmpliGone

Please see the documentation for more information as well as extended installation instructions and usage instructions.

AmpliGone is freely available under the AGPLv3 license.

If you use AmpliGone in your work, please cite us as follows:

Zwagemaker, F., Hajji, K., Raaijmakers, G., Schmitz, D., Kroneman, A. AmpliGone [Computer software]. https://doi.org/10.5281/zenodo.7684307