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:
Dependencies
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: 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: Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018; 34:3094–3100.
Samtools: Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16):2078–9.
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: Quinlan AR, Hall IM. BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics. 2010; 26(6):841–2.
Kraken2: Wood DE, Lu J, Langmead B. Improved metagenomic analysis with Kraken 2. Genome Biol 20, 257 (2019).
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: 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: Ondov BD, Bergman NH, Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics 12, 385 (2011).
Clair3: 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 and Tablet, respectively.