_AlienDiscover_ is a command line program written in [Java](https://docs.oracle.com/en/java/) that quickly infer 3' alien oligonucleotide sequence(s) (e.g. adapters, primers, ...) from ([Illumina](https://www.illumina.com/)) short high-thoughput sequencing (HTS) reads, without any prior knowledge. _AlienDiscover_ is an alternative to the tool _Minion_ from the _Kraken_ suite ([Davis et al. 2013](https://doi.org/10.1016/j.ymeth.2013.06.027)).
_AlienDiscover_ is a command line program written in [Java](https://docs.oracle.com/en/java/) that quickly infer 3' alien oligonucleotide sequence(s) (e.g. adapters, primers, ...) from ([Illumina](https://www.illumina.com/)) short high-thoughput sequencing (HTS) reads, without any prior knowledge. _AlienDiscover_ is an alternative to the tool _Minion_ from the _Kraken_ suite ([Davis et al. 2013](https://doi.org/10.1016/j.ymeth.2013.06.027)). Inferred alien oligonucleotide sequence(s) can next be clipped using e.g. [AlienTrimmer](https://gitlab.pasteur.fr/GIPhy/AlienTrimmer).
