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mq_saccharopolyspora

Summary report for project mq_saccharopolyspora. Generated using BGCFlow v0.9.0

Project Description

  • 26 Saccharopolysopra genomes of medium to high quality with less than 50 contigs. The new cutoff now removes GCF_000710755.1, GCF_015209505.1, GCF_014646075.1 and adds GCF_014697215.1
  • Sample size 26

Available reports

BGCFlow_rules description
seqfu Calculate sequence statistics using SeqFu.
mash Calculate distance estimation for all samples using MinHash.
fastani Do pairwise Average Nucleotide Identity (ANI) calculation across all samples.
checkm Assess genome quality with CheckM.
prokka-gbk Copy annotated genbank results.
antismash Summarizes antiSMASH result.
query-bigslice Map BGCs to BiG-FAM database (https://bigfam.bioinformatics.nl/)
bigscape Cluster BGCs using BiG-SCAPE
bigslice Cluster BGCs using BiG-SLiCE (https://github.com/medema-group/bigslice)
automlst-wrapper Simplified Tree building using autoMLST
arts Run Antibiotic Resistant Target Seeker (ARTS) on samples.
roary Build pangenome using Roary.
eggnog-roary Annotate Roary output using eggNOG mapper
deeptfactor Use deep learning to find Transcription Factors.
cblaster-genome Build diamond database of genomes for cblaster search.
cblaster-bgc Build diamond database of BGCs for cblaster search.
gecco GEne Cluster prediction with COnditional random fields.

References

If you find BGCFlow useful, please cite:

  • Nuhamunada, M., B.O. Palsson, O. S. Mohite, and T. Weber. 2022. BGCFlow [Computer software]. GITHUB: https://github.com/NBChub/bgcflow

  • Mölder, F., Jablonski, K.P., Letcher, B., Hall, M.B., Tomkins-Tinch, C.H., Sochat, V., Forster, J., Lee, S., Twardziok, S.O., Kanitz, A., Wilm, A., Holtgrewe, M., Rahmann, S., Nahnsen, S., Köster, J., 2021. Sustainable data analysis with Snakemake. F1000Res 10, 33.

  • Nathan C Sheffield, Michał Stolarczyk, Vincent P Reuter, André F Rendeiro, Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects, GigaScience, Volume 10, Issue 12, December 2021, giab077

Please also cite each tools used in the analysis:

  • Gilchrist, C., Booth, T. J., van Wersch, B., van Grieken, L., Medema, M. H., & Chooi, Y. (2021). cblaster: a remote search tool for rapid identification and visualisation of homologous gene clusters (Version 1.3.9) [Computer software]. https://doi.org/10.1101/2020.11.08.370601

  • Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, Sandra Reuter, Matthew T. G. Holden, Maria Fookes, Daniel Falush, Jacqueline A. Keane, Julian Parkhill, 'Roary: Rapid large-scale prokaryote pan genome analysis', Bioinformatics, 2015;31(22):3691-3693 doi:10.1093/bioinformatics/btv421

  • Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2014. Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Research, 25: 1043-1055.

  • Mungan,M.D., Alanjary,M., Blin,K., Weber,T., Medema,M.H. and Ziemert,N. (2020) ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining. Nucleic Acids Res.,10.1093/nar/gkaa374

  • Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2015).

  • Accurate de novo identification of biosynthetic gene clusters with GECCO. Laura M Carroll, Martin Larralde, Jonas Simon Fleck, Ruby Ponnudurai, Alessio Milanese, Elisa Cappio Barazzone, Georg Zeller. bioRxiv 2021.05.03.442509; doi:10.1101/2021.05.03.442509

  • Kim G.B., Gao Y., Palsson B.O., Lee S.Y. 2020. DeepTFactor: A deep learning-based tool for the prediction of transcription factors. PNAS. doi: 10.1073/pnas.2021171118

  • Telatin, A., Birolo, G., & Fariselli, P. SeqFu [Computer software]. GITHUB: https://github.com/telatin/seqfu2

  • Navarro-Muñoz, J.C., Selem-Mojica, N., Mullowney, M.W. et al. A computational framework to explore large-scale biosynthetic diversity. Nat Chem Biol 16, 60–68 (2020)

  • antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Kai Blin, Simon Shaw, Hannah E Augustijn, Zachary L Reitz, Friederike Biermann, Mohammad Alanjary, Artem Fetter, Barbara R Terlouw, William W Metcalf, Eric J N Helfrich, Gilles P van Wezel, Marnix H Medema, Tilmann Weber. Nucleic Acids Research (2023) doi: 10.1093/nar/gkad344

  • Mash: fast genome and metagenome distance estimation using MinHash. Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM. Genome Biol. 2016 Jun 20;17(1):132. doi: 10.1186/s13059-016-0997-x.

  • Satria A Kautsar, Justin J J van der Hooft, Dick de Ridder, Marnix H Medema, BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters, GigaScience, Volume 10, Issue 1, January 2021, giaa154

  • Mohammad Alanjary, Katharina Steinke, Nadine Ziemert, AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential,Nucleic Acids Research, Volume 47, Issue W1, 02 July 2019, Pages W276–W282

  • Satria A Kautsar, Justin J J van der Hooft, Dick de Ridder, Marnix H Medema, BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters, GigaScience, Volume 10, Issue 1, January 2021, giaa154.

  • Satria A Kautsar, Kai Blin, Simon Shaw, Tilmann Weber, Marnix H Medema, BiG-FAM: the biosynthetic gene cluster families database, Nucleic Acids Research, gkaa812, https://doi.org/10.1093/nar/gkaa812

  • Alanjary,M., Kronmiller,B., Adamek,M., Blin,K., Weber,T., Huson,D., Philmus,B. and Ziemert,N. (2017) The Antibiotic Resistant Target Seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery. Nucleic Acids Res.,10.1093/nar/gkx360

  • eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Carlos P. Cantalapiedra, Ana Hernandez-Plaza, Ivica Letunic, Peer Bork, Jaime Huerta-Cepas. 2021. Molecular Biology and Evolution, msab293

  • eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Jaime Huerta-Cepas, Damian Szklarczyk, Davide Heller, Ana Hernández-Plaza, Sofia K Forslund, Helen Cook, Daniel R Mende, Ivica Letunic, Thomas Rattei, Lars J Jensen, Christian von Mering, Peer Bork Nucleic Acids Res. 2019 Jan 8; 47(Database issue): D309–D314. doi: 10.1093/nar/gky1085

  • Mash Screen: high-throughput sequence containment estimation for genome discovery. Ondov BD, Starrett GJ, Sappington A, Kostic A, Koren S, Buck CB, Phillippy AM. Genome Biol. 2019 Nov 5;20(1):232. doi: 10.1186/s13059-019-1841-x.

  • Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014 Jul 15;30(14):2068-9. PMID:24642063

  • Jain, C., Rodriguez-R, L.M., Phillippy, A.M. et al. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 9, 5114 (2018). https://doi.org/10.1038/s41467-018-07641-9

  • antiSMASH 6.0: improving cluster detection and comparison capabilities. Kai Blin, Simon Shaw, Alexander M Kloosterman, Zach Charlop-Powers, Gilles P van Weezel, Marnix H Medema, & Tilmann Weber. Nucleic Acids Research (2021) doi: 10.1093/nar/gkab335.