diff --git a/CITATIONS.md b/CITATIONS.md index 1018ccd..6e43999 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -13,9 +13,25 @@ - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) + > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. -* [Porechop](https://github.com/rrwick/Porechop) +- [fastp](https://doi.org/10.1093/bioinformatics/bty560) + + > Chen, Shifu, Yanqing Zhou, Yaru Chen, and Jia Gu. 2018. “Fastp: An Ultra-Fast All-in-One FASTQ Preprocessor.” Bioinformatics 34 (17): i884-90. 10.1093/bioinformatics/bty560. + +- [AdapterRemoval2](https://doi.org/10.1186/s13104-016-1900-2) + + > Schubert, Mikkel, Stinus Lindgreen, and Ludovic Orlando. 2016. “AdapterRemoval v2: Rapid Adapter Trimming, Identification, and Read Merging.” BMC Research Notes 9 (February): 88. doi:10.1186/s13104-016-1900-2. + +- [Porechop](https://github.com/rrwick/Porechop) + +- [Kraken2](https://doi.org/10.1186/s13059-019-1891-0) + + > Wood, Derrick E., Jennifer Lu, and Ben Langmead. 2019. “Improved Metagenomic Analysis with Kraken 2.” Genome Biology 20 (1): 257. doi: 10.1186/s13059-019-1891-0. + +- [MALT](https://doi.org/10.1038/s41559-017-0446-6) + > Vågene, Åshild J., Alexander Herbig, Michael G. Campana, Nelly M. Robles García, Christina Warinner, Susanna Sabin, Maria A. Spyrou, et al. 2018. “Salmonella Enterica Genomes from Victims of a Major Sixteenth-Century Epidemic in Mexico.” Nature Ecology & Evolution 2 (3): 520-28. doi: 10.1038/s41559-017-0446-6. ## Software packaging/containerisation tools diff --git a/modules.json b/modules.json index c4b2f12..dcfbd3f 100644 --- a/modules.json +++ b/modules.json @@ -35,4 +35,4 @@ } } } -} \ No newline at end of file +}