v.2.0.1

Job 9c2cb5d3 - Saccharomyces species

Status
Finished
Finished at
2021/06/07 11:22
Run time
104.62 min

Comparative Genomics results

Your prediction results are ready and at least available until 2021/20/07 11:22.

Click on a button to receive the related results.


BUSCO
Completeness (HTML) Missing (HTML)
Completeness
Missing BUSCOs
EukCC
Completeness (HTML)


ANI
Raw file Visual file Heatmap (HTML)

Query genomeReference genomeANI valueBidirectional fragmentsTotal fragments
Saccharomyces arboricolaSaccharomyces cerevisiae80.411227863854
Saccharomyces arboricolaSaccharomyces eubayanus80.843529553854
Saccharomyces arboricolaSaccharomyces kudriavzevii81.744131783854
Saccharomyces arboricolaSaccharomyces mikatae80.345422783854
Saccharomyces arboricolaSaccharomyces paradoxus81.086330093854
Saccharomyces arboricolaSaccharomyces uvarum81.052929303854
Saccharomyces cerevisiaeSaccharomyces arboricola80.452627344045
Saccharomyces cerevisiaeSaccharomyces eubayanus79.680724654045
Saccharomyces cerevisiaeSaccharomyces kudriavzevii80.890929514045
Saccharomyces cerevisiaeSaccharomyces mikatae82.344926504045
Saccharomyces cerevisiaeSaccharomyces paradoxus88.222537054045
Saccharomyces cerevisiaeSaccharomyces uvarum79.589825464045
Saccharomyces eubayanusSaccharomyces arboricola80.899729293899
Saccharomyces eubayanusSaccharomyces cerevisiae79.646624973899
Saccharomyces eubayanusSaccharomyces kudriavzevii80.669728913899
Saccharomyces eubayanusSaccharomyces mikatae79.682720053899
Saccharomyces eubayanusSaccharomyces paradoxus80.087827043899
Saccharomyces eubayanusSaccharomyces uvarum91.139536403899
Saccharomyces kudriavzeviiSaccharomyces arboricola81.739331443942
Saccharomyces kudriavzeviiSaccharomyces cerevisiae80.807929903942
Saccharomyces kudriavzeviiSaccharomyces eubayanus80.667428853942
Saccharomyces kudriavzeviiSaccharomyces mikatae80.804323823942
Saccharomyces kudriavzeviiSaccharomyces paradoxus81.654231563942
Saccharomyces kudriavzeviiSaccharomyces uvarum80.92328673942
Saccharomyces mikataeSaccharomyces arboricola80.263923193079
Saccharomyces mikataeSaccharomyces cerevisiae82.356126583079
Saccharomyces mikataeSaccharomyces eubayanus79.592320453079
Saccharomyces mikataeSaccharomyces kudriavzevii80.771324163079
Saccharomyces mikataeSaccharomyces paradoxus83.59827993079
Saccharomyces mikataeSaccharomyces uvarum79.690720273079
Saccharomyces paradoxusSaccharomyces arboricola81.048429884023
Saccharomyces paradoxusSaccharomyces cerevisiae88.231537004023
Saccharomyces paradoxusSaccharomyces eubayanus80.085927304023
Saccharomyces paradoxusSaccharomyces kudriavzevii81.598131834023
Saccharomyces paradoxusSaccharomyces mikatae83.606227484023
Saccharomyces paradoxusSaccharomyces uvarum80.186927184023
Saccharomyces uvarumSaccharomyces arboricola81.049229343847
Saccharomyces uvarumSaccharomyces cerevisiae79.661425183847
Saccharomyces uvarumSaccharomyces eubayanus91.162336573847
Saccharomyces uvarumSaccharomyces kudriavzevii80.941928773847
Saccharomyces uvarumSaccharomyces mikatae79.642520693847
Saccharomyces uvarumSaccharomyces paradoxus80.218626673847


Please cite always:
Roman Martin, Thomas Hackl, Georges Hattab, Matthias G Fischer, Dominik Heider (2020). MOSGA: Modular Open-Source Genome Annotator. Bioinformatics. 36(22-23). 5514–5515. doi: 10.1093/bioinformatics/btaa1003.

Do you have some questions, issues or just would like to give us feedback? Please don't hesitate to write us or feel free to open a new issue on Gitlab.

Snakemake configuration Snakemake log What to cite

Single outputs
BUSCO genes BUSCOs category (HTML) BUSCOs missing (HTML) EukCC genes EukCC completeness (HTML) FastANI results FastANI visual file FastANI values (HTML) trimAl output MAFFT output

What to cite
Saary P, Mitchell AL, Finn RD. Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC. Genome Biol. 2020 10;21(1):244. doi: 10.1186/s13059-020-02155-4.
Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006 1;22(21):2688-90. doi: 10.1093/bioinformatics/btl446.
Yu G, Smith D, Zhu H, Guan Y, Lam T T. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data (2017). Methods in Ecology and Evolution, 8(1):28-36. doi:10.1111/2041-210X.12628
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013 ;30(4):772-80. doi: 10.1093/molbev/mst010.
Matsen FA, Kodner RB, Armbrust EV. pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree (2010). BMC Bioinformatics. 11:538. doi: 10.1186/1471-2105-11-538
Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002 15;30(14):3059-66. doi: 10.1093/nar/gkf436.
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014 1;30(9):1312-3. doi: 10.1093/bioinformatics/btu033.
Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015 1;31(19):3210-2. doi: 10.1093/bioinformatics/btv351.
Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009 1;25(15):1972-3. doi: 10.1093/bioinformatics/btp348.
Martin R, Hackl T, Hattab G, Fischer MG, Heider D. MOSGA: Modular Open-Source Genome Annotator. Bioinformatics. 2021;36(22-23):5514-5515. doi: 10.1093/bioinformatics/btaa1003
Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018 30;9(1):5114. doi: 10.1038/s41467-018-07641-9.
Waterhouse RM, Seppey M, Simão FA, Manni M, Ioannidis P, Klioutchnikov G, Kriventseva EV, Zdobnov EM. BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics. Mol Biol Evol. 2018 1;35(3):543-548. doi: 10.1093/molbev/msx319.



Upload your assembled FASTA genome file.

Priority (highest priority first)

    Functional Enrichment Analysis


    Protein-Protein Interactions Analysis


    Protein-Protein Interactions Analysis


    Choose your tools:

    Genes

    Gene
    Gene prediction tool

    Prediction of gene locations and splicing sites.

    Mode of work

    Evidence-based or ab initio prediction

    Functional prediction

    Functional gene prediction by comparison of protein databases.

    Repeats

    Repeats

    Detection of repeating sequences.

    tRNAs

    tRNA

    Prediction of tRNA sequences.

    rRNAs

    rRNA

    Search for rRNA sequence matches.

    Assembly Validation

    Genome Completeness

    Validate genome completeness.

    Quality-Control

    Contamination Detection and Assembly Quality


    UID Name FASTA files Submission Date Start date End date Mode Status

    The Modular Open-Source Genome Annotator (MOSGA) is a pipeline that easily creates draft genome annotation by a graphical user interface. It combines several specific prediction tools and generates a submission-ready annotation file.

    The source code is freely available on Gitlab.com. We recommend building a new docker container from the available Dockerfile in the linked Gitlab repository. MOSGA is written modular and allows easy integration of new prediction tools or even including whole third-party pipelines.

    For any questions or comments, please contact us: roman.martin@uni-marburg.de. We are happy to receive new suggestions or even merge requests for a pipeline extension. To provide an overview of the operation principle, we recommend reading our Gitlab wiki page.

    We are providing an example data set of the draft genome annotation of Cafeteria roenbergensis BVI strain. Initially, we used an early version of MOSGA to annotate this genome (Hackl et al., 2020). Hackl, T., Martin, R., Barenhoff, K. et al. Four high-quality draft genome assemblies of the marine heterotrophic nanoflagellate Cafeteria roenbergensis. Sci Data 7, 29 (2020).

    We provide two examples for the comparative genomics workflow: The Saccharomyces species phylogenetics and the Saccharomyces gene comparison. An exemplary annotation job for the organelle scanner based on the Nannochloropsis oceanica genome is here available.

    Please take care about the licenses of the selected tools.

    Whenever you use MOSGA please cite us:
    Roman Martin orcid, Thomas Hackl orcid, Georges Hattab orcid, Matthias Fischer orcid, Dominik Heider orcid (2020). MOSGA: Modular Open-Source Genome Annotator. Bioinformatics. 36(22-23). 5514–5515. doi: 10.1093/bioinformatics/btaa1003.

    This MOSGA instance is hosted by the Philipps University of Marburg for demonstration purposes.
    It runs on an AMD Zen processor with 16 threads and 32 GB of memory.

    Processed jobs that are older than 14 days will be deleted automatically.

    Incoming jobs are queued and processed as soon as possible. Jobs that stress our hardware longer than 48 hours could be terminated.

    Uploading jobs could be aborted depending on your bandwidth and the upload duration. Therefore we recommend not to upload files that are larger than 200 MiB.

    We reserve the right to analyze failed jobs to determine errors and to provide bug fixes and quality improvements. Your results will still not be shared and regularly delete.

    If you provide a notification email address we may contact you then we could detect that could be avoided or fixed.


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