Underlying tools

The microGWAS pipeline uses a number of computational tools underneath, which you should try to cite in any publication that uses the results produced by the pipeline.

Tip

If you are the author of one the tools and spot an error in the references, please get in touch by opening an issue on the repository.

• unitig-counter: 10.1371/journal.pgen.1007758 and 10.1128/mbio.01344-20

• mlst: Seemann T, mlst and 10.12688/wellcomeopenres.14826.1

• abritamr: 10.1038/s41467-022-35713-4

• mash: 10.1186/s13059-016-0997-x

• ggCaller: 10.1101/gr.277733.123

• panaroo: 10.1186/s13059-020-02090-4

• fasttree: 10.1371/journal.pone.0009490

• snp-sites: 10.1099/mgen.0.000056

• snippy: Seemann T, snippy

• bcftools: 10.1093/gigascience/giab008

• limix: 10.1101/003905

• ALBI: 10.1016/j.ajhg.2016.04.016

• sequence_unet: 10.1186/s13059-023-02948-3

• pyseer: 10.1093/bioinformatics/bty539 and 10.1101/852426

• bwa: 10.48550/arXiv.1303.3997

• bedtools: 10.1093/bioinformatics/btq033 and 10.1093/bioinformatics/btr539

• eggnog-mapper: 10.1093/molbev/msx148

• panfeed: 10.1099/mgen.0.001129