# Citation

A scientific publication fully describing this pipeline is being prepared. Meanwhile, feel free to cite this GitHub repository. Primary references for the dependencies used should also be cited:

## ViralUnity

In preparation.

## Dependencies

**[fastp](https://github.com/OpenGene/fastp):** Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. *Bioinformatics*. 2018; 34(17):i884–i890.

**[MultiQC](https://github.com/ewels/MultiQC):** Ewels P, Magnusson M, Lundin S, et al. MultiQC: Summarize analysis results for multiple tools and samples in a single report. *Bioinformatics*. 2016; 32(19):3047–8.

**[Minimap2](https://github.com/lh3/minimap2):** Li H. Minimap2: pairwise alignment for nucleotide sequences. *Bioinformatics*. 2018; 34:3094–3100.

**[Samtools](https://github.com/samtools/samtools):** Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment/Map format and SAMtools. *Bioinformatics*. 2009; 25(16):2078–9.

**[iVar](https://github.com/andersen-lab/ivar):** Grubaugh ND, Gangavarapu K, Quick J, et al. An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar. *Genome Biol* 20, 8 (2019).

**[BEDtools](https://github.com/arq5x/bedtools2):** Quinlan AR, Hall IM. BEDTools: A flexible suite of utilities for comparing genomic features. *Bioinformatics*. 2010; 26(6):841–2.

**[Kraken2](https://doi.org/10.1186/s13059-019-1891-0):** Wood DE, Lu J, Langmead B. Improved metagenomic analysis with Kraken 2. *Genome Biol* 20, 257 (2019).

**[DIAMOND](https://github.com/bbuchfink/diamond):** Buchfink B, Reuter K, Drost H-G. Sensitive protein alignments at tree-of-life scale using DIAMOND. *Nature Methods* 18, 366–368 (2021).

**[MEGAHIT](https://github.com/voutcn/megahit):** Li D, Liu C-M, Luo R, Sadakane K, Lam T-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. *Bioinformatics*. 2015; 31(10):1674–1676.

**[Krona](https://doi.org/10.1186/1471-2105-12-385):** Ondov BD, Bergman NH, Phillippy AM. Interactive metagenomic visualization in a Web browser. *BMC Bioinformatics* 12, 385 (2011).

**[Clair3](https://www.nature.com/articles/s43588-022-00387-x):** Zheng, Z., Li, S., Su, J. et al. Symphonizing pileup and full-alignment for deep learning-based long-read variant calling. *Nature Computational Science* 2, 797–803 (2022).

For visualization of FASTA and BAM files, we recommend [AliView](https://ormbunkar.se/aliview/) and [Tablet](https://ics.hutton.ac.uk/tablet/), respectively.