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Citations

Viralgenie

!!! warning Viralgenie is currently not Published. Please cite as:

- Klaps J, Lemey P, Kafetzopoulou L. Viralgenie: A metagenomics analysis pipeline for eukaryotic viruses. __Github__ https://github.com/Joon-Klaps/viralgenie

nf-core

Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.

Nextflow

Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.

Pipeline tools

  • Bbduk

    Bushnell B. (2022) BBMap, URL: http://sourceforge.net/projects/bbmap/

  • BCFtools

    Danecek, Petr et al. “Twelve years of SAMtools and BCFtools.” GigaScience vol. 10,2 (2021): giab008. doi:10.1093/gigascience/giab008

  • blast

    Camacho, Christiam et al. “BLAST+: architecture and applications.” BMC bioinformatics vol. 10 421. 15 Dec. 2009, doi:10.1186/1471-2105-10-421

  • Bowtie2

    Langmead, Ben, and Steven L Salzberg. “Fast gapped-read alignment with Bowtie 2.” Nature methods vol. 9,4 357-9. 4 Mar. 2012, doi:10.1038/nmeth.1923

  • BWA-MEM

    Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997v2.

  • BWA-MEM2

    M. Vasimuddin, S. Misra, H. Li and S. Aluru, "Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems," 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS), Rio de Janeiro, Brazil, 2019, pp. 314-324, doi: 10.1109/IPDPS.2019.00041.

  • cdhit

    Fu, Limin et al. “CD-HIT: accelerated for clustering the next-generation sequencing data.” Bioinformatics (Oxford, England) vol. 28,23 (2012): 3150-2. doi:10.1093/bioinformatics/bts565

  • checkv

    Nayfach, Stephen et al. “CheckV assesses the quality and completeness of metagenome-assembled viral genomes.” Nature biotechnology vol. 39,5 (2021): 578-585. doi:10.1038/s41587-020-00774-7

  • FastQC

    Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].

  • fastp

    Chen, Shifu et al. “fastp: an ultra-fast all-in-one FASTQ preprocessor.” Bioinformatics (Oxford, England) vol. 34,17 (2018): i884-i890. doi:10.1093/bioinformatics/bty560

  • HUMID

    Laros J, van den Berg R, Github https://github.com/jfjlaros/HUMID

  • iVar

    Grubaugh, Nathan D et al. “An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar.” Genome biology vol. 20,1 8. 8 Jan. 2019, doi:10.1186/s13059-018-1618-7

  • Kaiju

    Menzel, Peter et al. “Fast and sensitive taxonomic classification for metagenomics with Kaiju.” Nature communications vol. 7 11257. 13 Apr. 2016, doi:10.1038/ncomms11257

  • Kraken2

    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.

  • leiden-algorithm

    Traag, V A et al. “From Louvain to Leiden: guaranteeing well-connected communities.” Scientific reports vol. 9,1 5233. 26 Mar. 2019, doi:10.1038/s41598-019-41695-z

  • Mash

    Ondov, Brian D et al. “Mash: fast genome and metagenome distance estimation using MinHash.” Genome biology vol. 17,1 132. 20 Jun. 2016, doi:10.1186/s13059-016-0997-x

  • Megahit

    Li, Dinghua et al. “MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices.” Methods (San Diego, Calif.) vol. 102 (2016): 3-11. doi:10.1016/j.ymeth.2016.02.020

  • Minimap2

    Li, Heng. “Minimap2: pairwise alignment for nucleotide sequences.” Bioinformatics (Oxford, England) vol. 34,18 (2018): 3094-3100. doi:10.1093/bioinformatics/bty191

  • MMseqs2

    Steinegger, Martin, and Johannes Söding. “MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets.” Nature biotechnology vol. 35,11 (2017): 1026-1028. doi:10.1038/nbt.3988

  • Mosdepth

    Pedersen, Brent S, and Aaron R Quinlan. “Mosdepth: quick coverage calculation for genomes and exomes.” Bioinformatics (Oxford, England) vol. 34,5 (2018): 867-868. doi:10.1093/bioinformatics/btx699

  • MultiQC

    Ewels, Philip et al. “MultiQC: summarize analysis results for multiple tools and samples in a single report.” Bioinformatics (Oxford, England) vol. 32,19 (2016): 3047-8. doi:10.1093/bioinformatics/btw354

  • picard-tools

  • QUAST

    Gurevich, Alexey et al. “QUAST: quality assessment tool for genome assemblies.” Bioinformatics (Oxford, England) vol. 29,8 (2013): 1072-5. doi:10.1093/bioinformatics/btt086

  • SAMtools

    Li H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011 Nov 1;27(21):2987-93. doi: 10.1093/bioinformatics/btr509. Epub 2011 Sep 8. PMID: 21903627; PMCID: PMC3198575.

  • SPAdes

    Bankevich, Anton et al. “SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.” Journal of computational biology : a journal of computational molecular cell biology vol. 19,5 (2012): 455-77. doi:10.1089/cmb.2012.0021

  • SSPACE Basic

    Boetzer, Marten et al. “Scaffolding pre-assembled contigs using SSPACE.” Bioinformatics (Oxford, England) vol. 27,4 (2011): 578-9. doi:10.1093/bioinformatics/btq683

  • Trimmomatic

    Bolger, Anthony M et al. “Trimmomatic: a flexible trimmer for Illumina sequence data.” Bioinformatics (Oxford, England) vol. 30,15 (2014): 2114-20. doi:10.1093/bioinformatics/btu170

  • Trinity

    Haas, Brian J et al. “De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.” Nature protocols vol. 8,8 (2013): 1494-512. doi:10.1038/nprot.2013.084

  • UMI-tools

    Smith, Tom et al. “UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy.” Genome research vol. 27,3 (2017): 491-499. doi:10.1101/gr.209601.116

  • vRhyme

    Kieft, Kristopher et al. “vRhyme enables binning of viral genomes from metagenomes.” Nucleic acids research vol. 50,14 (2022): e83. doi:10.1093/nar/gkac341

  • VSEARCH

    Rognes, Torbjørn et al. “VSEARCH: a versatile open source tool for metagenomics.” PeerJ vol. 4 e2584. 18 Oct. 2016, doi:10.7717/peerj.2584

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, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.

  • BioContainers

    da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.

  • Docker

    Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.

  • Singularity

    Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.