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 both 'end-to-end' as well as 'end-to-mid' amplicons to be cleaned. Please see this page to learn more about this terminology.

Please see the installation instructions page in order to get started quickly, or see our user guide page to learn how to best use AmpliGone for your analysis.

AmpliGone is freely available under the AGPLv3 licence