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References

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  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/)

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  8. Andrews,S. (2010) FastQC: A Quality Control tool for High Throughput Sequence Data.

  9. Ewels,P., Magnusson,M., Lundin,S. and Käller,M. (2016) MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics, 32, 3047–3048.

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