CITATIONS.md

Arcadia-Science/prehgt: Citations

A number of tools were used to make the prehgt pipeline. Depending on how you use the prehgt pipeline, please consider citing the papers and resources below.

Workflow tools

• nf-core

  Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. (2020). The nf-core framework for community-curated bioinformatics pipelines. https://doi.org/10.1038/s41587-020-0439-x

• Nextflow

  Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. (2017). Nextflow enables reproducible computational workflows. https://doi.org/10.1038/nbt.3820

• Snakemake

  Köster J, Rahmann S. (2012). Snakemake—a scalable bioinformatics workflow engine. https://doi.org/10.1093/bioinformatics/bts480

Pipeline tools

• csvtk

• DIAMOND

  Buchfink B, Xie C, Huson DH. (2014). Fast and sensitive protein alignment using DIAMOND. https://doi.org/10.1038/nmeth.3176

• EMBOSS

  Rice P, Longden I, Bleasby A. (2000). EMBOSS: the European molecular biology open software suite.

• fastcluster

  Müllner D. (2013). fastcluster: Fast Hierarchical, Agglomerative Clustering. https://doi.org/10.18637/jss.v053.i09

• HMMER3

• KofamScan

  Aramaki T, Blanc-Mathieu R, Endo H, Ohkubo K, Kanehisa M, Goto S, Ogata H. (2020). KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold. https://doi.org/10.1093/bioinformatics/btz859

• MMSeq2

  Steinegger M, Söding J. (2017). MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. https://doi.org/10.1038/nbt.3988

• ncbi-genome-download

• seqtk

• tidyverse

  Wickham H, Averick M, Bryan J, Chang W, McGowan LD, François R, Grolemund G, Hayes A, Henry L, Hester J, Kuhn M. (2019). Welcome to the Tidyverse. https://doi.org/10.21105/joss.01686

Horizontal gene transfer prediction algorithms

• Alien index

  Gladyshev EA, Meselson M, Arkhipova IR. (2008). Massive horizontal gene transfer in bdelloid rotifers. https://doi.org/10.1126/science.1156407

• Donor distribution index

  Ma J, Wang S, Zhu X, Sun G, Chang G, Li L, Hu X, Zhang S, Zhou Y, Song CP, Huang J. (2022). Major episodes of horizontal gene transfer drove the evolution of land plants. https://doi.org/10.1016/j.molp.2022.02.001

• HGT score

  Boschetti C, Carr A, Crisp A, Eyres I, Wang-Koh Y, Lubzens E, Barraclough TG, Micklem G, Tunnacliffe A. (2012). Biochemical diversification through foreign gene expression in bdelloid rotifers. https://doi.org/10.1371/journal.pgen.1003035

• Transfer index

  Nguyen M, Ekstrom A, Li X, Yin Y. (2015). HGT-Finder: A new tool for horizontal gene transfer finding and application to Aspergillus genomes. https://doi.org/10.3390/toxins7104035

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. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. https://doi.org/10.1038/s41592-018-0046-7

• 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. (2017). BioContainers: an open-source and community-driven framework for software standardization. https://doi.org/10.1093/bioinformatics/btx192