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References

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This documentation is for AMR++ version 2.0. Click here for the latest docs.

  1. Bolger,A.M., Lohse,M. and Usadel,B. (2014) Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics, 10.1093/bioinformatics/btu170.

  2. Li,H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. ArXiv13033997 Q-Bio.

  3. Quinlan,A.R. and Hall,I.M. (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26, 841–842.

  4. Li,H., Handsaker,B., Wysoker,A., Fennell,T., Ruan,J., Homer,N., Marth,G., Abecasis,G., Durbin,R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence Alignment/Map format and SAMtools. Bioinforma. Oxf. Engl., 25, 2078–2079.

  5. Wood,D.E., Lu,J. and Langmead,B. (2019) Improved metagenomic analysis with Kraken 2. bioRxiv, 10.1101/762302.

  6. Nextflow programming language (https://www.nextflow.io/)

  7. Singularity: Scientific containers for mobility of compute. (https://singularity.lbl.gov/)