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deng-lab/viroprofiler: Citations

Software Module License
metaSPAdes Assembly NA
vRhyme Binning GPL v3
Phamb Binning MIT License
CheckV Virus detection and QC BSD license
VirSorter2 Virus detection GPL v2
DeepVirFinder Virus detection USC-RL v1.0
VIBRANT Virus detection and gene annotation GPL v3
DRAM Gene annotation GPL v3
eggnog-mapper Gene annotation GPL v3
abricate Gene annotation GPL v2
MMseqs2 Taxonomy assignment GPL v3
vConTACT2 Taxonomy assignment GPL v3
Bacphlip Lifestyle prediction MIT License
Replidec Lifestyle prediction MIT License
iPHoP Host prediction GPL v3
CoverM Abundance estimation GPL v3
Kraken2 Taxonomy assignment MIT License
Bracken Abundance estimation GPL v3

nf-core

Ewels, Philip A., et al. "The nf-core framework for community-curated bioinformatics pipelines." Nature biotechnology 38.3 (2020): 276-278.

Nextflow

Di Tommaso, Paolo, et al. "Nextflow enables reproducible computational workflows." Nature biotechnology 35.4 (2017): 316-319.

Pipeline tools

  • FastQC

  • fastp

    Chen, Shifu, et al. "fastp: an ultra-fast all-in-one FASTQ preprocessor." Bioinformatics 34.17 (2018): i884-i890.

  • BBMap

    Bushnell, Brian. BBMap: a fast, accurate, splice-aware aligner. No. LBNL-7065E. Lawrence Berkeley National Lab.(LBNL), Berkeley, CA (United States), 2014.

  • metaSPAdes

    Nurk, Sergey, et al. "metaSPAdes: a new versatile metagenomic assembler." Genome research 27.5 (2017): 824-834.

  • Bowtie 2

    Langmead, Ben, and Steven L. Salzberg. "Fast gapped-read alignment with Bowtie 2." Nature methods 9.4 (2012): 357-359.

  • CoverM

  • CheckV

    Nayfach, Stephen, et al. "CheckV assesses the quality and completeness of metagenome-assembled viral genomes." Nature biotechnology 39.5 (2021): 578-585.

  • VirSorter2

    Guo, Jiarong, et al. "VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses." Microbiome 9.1 (2021): 1-13.

  • DeepVirFinder

    Ren, Jie, et al. "Identifying viruses from metagenomic data using deep learning." Quantitative Biology 8.1 (2020): 64-77.

  • VIBRANT

    Kieft, Kristopher, Zhichao Zhou, and Karthik Anantharaman. "VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences." Microbiome 8.1 (2020): 1-23.

  • vRhyme

    Kieft K, Adams A, Salamzade R, et al. vRhyme enables binning of viral genomes from metagenomes[J]. Nucleic Acids Research, 2022, 50(14): e83-e83.

  • Phamb

    Johansen, Joachim, et al. "Genome binning of viral entities from bulk metagenomics data." Nature communications 13.1 (2022): 1-12.

  • DRAM-v

    Shaffer, Michael, et al. "DRAM for distilling microbial metabolism to automate the curation of microbiome function." Nucleic acids research 48.16 (2020): 8883-8900.

  • vConTACT2

    Bin Jang, Ho, et al. "Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks." Nature biotechnology 37.6 (2019): 632-639.

  • MMseqs2

    Steinegger, Martin, and Johannes Söding. "MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets." Nature biotechnology 35.11 (2017): 1026-1028. Mirdita, Milot, et al. "Fast and sensitive taxonomic assignment to metagenomic contigs." Bioinformatics 37.18 (2021): 3029-3031.

  • eggNOG-mapper

    Cantalapiedra C P, Hernández-Plaza A, Letunic I, et al. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale[J]. Molecular biology and evolution, 2021, 38(12): 5825-5829.

  • abricate

  • iPHoP

    Roux S, Camargo AP, Coutinho FH, Dabdoub SM, Dutilh BE, Nayfach S, Tritt A. iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria. PLoS biology. 2023 Apr 21;21(4):e3002083.

  • bacphlip

    Hockenberry A J, Wilke C O. BACPHLIP: predicting bacteriophage lifestyle from conserved protein domains[J]. PeerJ, 2021, 9: e11396.

  • Replidec

    Peng, Xue, et al. "Replidec-Use naive Bayes classifier to identify virus lifecycle from metagenomics data." bioRxiv (2022): 2022-07.

  • Kraken2

    Wood, Derrick E., Jennifer Lu, and Ben Langmead. "Improved metagenomic analysis with Kraken 2." Genome biology 20 (2019): 1-13.

  • Bracken

    Lu, Jennifer, et al. "Bracken: estimating species abundance in metagenomics data." PeerJ Computer Science 3 (2017): e104.

  • MultiQC

    Ewels, Philip, et al. "MultiQC: summarize analysis results for multiple tools and samples in a single report." Bioinformatics 32.19 (2016): 3047-3048.

Software packaging/containerisation tools

  • Anaconda

    Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.

  • Bioconda

    Grüning B, Dale R, Sjödin A, et al. Bioconda: sustainable and comprehensive software distribution for the life sciences[J]. Nature methods, 2018, 15(7): 475-476.

  • BioContainers

    da Veiga Leprevost F, Grüning B A, Alves Aflitos S, et al. BioContainers: an open-source and community-driven framework for software standardization[J]. Bioinformatics, 2017, 33(16): 2580-2582.

  • Docker

    Merkel D. Docker: lightweight linux containers for consistent development and deployment[J]. Linux j, 2014, 239(2): 2.

  • Singularity

    Kurtzer G M, Sochat V, Bauer M W. Singularity: Scientific containers for mobility of compute[J]. PloS one, 2017, 12(5): e0177459.