2.6.0 (mosga.py)

Job dd02ad62 - Organelle Scanner

Status
Finished
Finished at
2021/19/07 15:45
Finished in
13 min

Annotation results

Your genome annotation results are ready and at least available until 2021/26/07 15:45.

Click on a button to receive the related files or view the results dynamically on the genome web browser.

SQN Submission File (NCBI) Genome Feature Table
View results online

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.
  • Roman Martin, Hagen Dreßler, Georges Hattab, Thomas Hackl, Matthias G Fischer, Dominik Heider (2021). MOSGA 2: Comparative genomics and validation tools. Computational and Structural Biotechnology Journal. 19. 5504-5509. doi: 10.1016/j.csbj.2021.09.024.

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.

BUSCO (genome)


Scaffold Repeats tRNA Total
Total 6966 24 6990
CP038106.1 281 0 281
CP038117.1 225 0 225
CP038128.1 288 1 289
CP038130.1 304 3 307
CP038131.1 280 0 280
CP038132.1 233 1 234
CP038133.1 310 0 310
CP038134.1 243 0 243
CP038135.1 271 0 271
CP038107.1 268 0 268
CP038108.1 270 0 270
CP038109.1 268 0 268
CP038110.1 239 1 240
CP038111.1 226 0 226
CP038112.1 236 0 236
CP038113.1 191 0 191
CP038114.1 248 0 248
CP038115.1 269 2 271
CP038116.1 222 0 222
CP038118.1 252 0 252
CP038119.1 151 1 152
CP038120.1 249 0 249
CP038121.1 189 0 189
CP038122.1 192 0 192
CP038123.1 184 0 184
CP038124.1 204 0 204
CP038125.1 177 0 177
CP038126.1 178 1 179
CP038127.1 179 0 179
CP038129.1 139 0 139
CP038137.1 0 5 5
CP038136.1 0 9 9

Taxonomy search result
Tool Hit NCBI-ID Distance
BUSCO eukaryota_odb10 2759 4
Annotation database Snakemake configuration Snakemake log Taxonomy Search Validation File Error Summary Discrepancy Report What to cite

Single outputs
Genome Annotation GFF Feature Table Writing Organelle Scan Mitos Plastids WindowMasker Import tRNAscan-SE 2 Import tRNAscan-SE 2 Results Barrnap Import Barrnap Results BUSCO Summary BUSCO Graph BUSCO Matches VecScreen Report VecScreen UniVec Raw Matches VecScreen UniVec Matches

What to cite
Seemann T. barrnap 0.9 : rapid ribosomal RNA prediction. https://github.com/tseemann/barrnap
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
Morgulis A, Gertz EM, Schäffer AA, Agarwala R (2006). WindowMasker: window-based masker for sequenced genomes. Bioinformatics. 22(2):134‐141.
Chan, P.P., Lin, B., and Lowe, T.M (2019). tRNAscan-SE 2.0: Improved Detection and Functional Classification of Transfer RNA Genes. BioRxiv. doi: 10.1101/614032
Buels R, Yao E, Diesh CM, Hayes RD, Munoz-Torres M, Helt G, Goodstein DM, Elsik CG, Lewis SE, Stein L, Holmes IH (2016). JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biol. 12;17:66. doi: 10.1186/s13059-016-0924-1
Nawrocki EP, Kolbe DL, Eddy SR. Infernal 1.0: inference of RNA alignments (2009). Bioinformatics 25(10):1335-7. Erratum in: Bioinformatics. 2009 Jul 1;25(13):1713. doi: 10.1093/bioinformatics/btp157

Upload your assembled FASTA eukaryotic genome file.

Needed for the GenBank/ENA submission files.
Assembly details for the submission (optional): GenBank needs all three as structured comment, ENA in the Webin-CLI manifest. MOSGA adds the annotation details itself.
Priority (highest priority first)
    Overlapping features
    How overlaps of these types are solved, only types of the selected tools are listed. Removed features are listed with the reason in removed.gff of the results. Overlapping rRNAs are always solved (table2asn rejects them).

    CpG island detection

    CpG island detection

    Splicing site detection

    Functional Enrichment Analysis

    Protein-Protein Interactions Analysis

    Protein-Protein Interactions Analysis

    Choose your tools:

    Genes

    Gene
    Protein-coding genes

    Prediction of gene locations and splice sites.

    Mode of work

    Evidence-based or ab initio prediction.

    Functional Annotation

    Functional gene prediction.

    Repeats

    Repeats

    Detection of repeating sequences.

    tRNAs

    tRNA

    Prediction of tRNA sequences.

    rRNAs

    rRNA

    Search for rRNA sequence matches.

    ncRNAs

    ncRNA

    Search for non-coding RNA genes.

    Telomeres

    Telomere

    Detection of telomeric repeats.

    Assembly Validation

    Genome Completeness

    Validate genome completeness.

    Annotation Statistics

    Statistics of the final annotation.

    Quality-Control

    Contamination detection.

    UID Name 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 or Zenodo.com (DOI: 10.5281/zenodo.5121228). 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.

    No command line

    Upload a genome, choose the tools with a click and follow the job in the browser.

    Submission-ready

    NCBI .sqn/.tbl and ENA EMBL with Webin manifest, a submission check tells what to fix.

    Modular tools

    Genes, repeats, tRNAs, rRNAs, ncRNAs and telomeres, freely combined from established predictors.

    Conflict resolution

    Overlaps are solved by type and tool priority, removed features are listed with the reason.

    Functional annotation

    Product names from Swiss-Prot, eggNOG and IDTAXA, names to review are flagged.

    Quality control

    BUSCO, EukCC, AGAT, BlobTools and VecScreen in the same job.

    Comparative genomics

    ANI, gene comparison, phylogenetic trees and completeness across genomes, also of earlier jobs.

    Organelle scan

    Finds likely mitochondrial and plastid scaffolds and suggests to submit them as organelle sequences.

    Interactive results

    JBrowse 2 genome browser, summaries and all files on one results page.

    One Docker image

    Pinned and checksum-verified tool versions for reproducible results, self-hosted so the data stays in-house.

    Convenient workflow

    Uploads of several GB in resumable parts, profiles per kind of job, "Submit again", retry of failed jobs and mail notification.

    Open source

    MIT licensed, the code is on GitLab and Zenodo, new tools and merge requests are welcome.

    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.

    Roman Martin orcid, Hagen Dreßler orcid, Georges Hattab orcid, Thomas Hackl orcid, Matthias Fischer orcid, Dominik Heider orcid (2021). MOSGA 2: Comparative genomics and validation tools. Computational and Structural Biotechnology Journal. 19. 5504-5509. doi: 10.1016/j.csbj.2021.09.024.

    The University of Münster hosts this MOSGA instance for demonstration purposes.
    It runs on a virtualized AMD Ryzen CPU with 8 cores and 32 GB of memory.

    We keep the 100 most recent job submissions online. Once this limit is exceeded, we delete the oldest job that is more than 14 days old. Incoming jobs are queued and processed as soon as possible. Jobs that occupy our hardware for more than 48 hours may be terminated. We recommend not uploading files larger than 2 GiB.

    We reserve the right to analyze failed jobs in order to identify errors and to provide bug fixes and quality improvements. Even so, your results will not be shared with anyone and will be deleted regularly.

    If you provide a notification email address, we may contact you if your job fails so that we can help resolve the issue.

    Imprint

    Universität Münster
    Medizinische Fakultät (Faculty of Medicine)
    Albert-Schweitzer-Campus 1, Building D3
    48149 Münster, Germany
    Phone: +49 251 83 52263
    Fax: +49 251 83 55004
    Email: dekanmed@ukmuenster.de

    The Faculty of Medicine is part of the University of Münster. The University of Münster is a corporation under public law (Körperschaft des öffentlichen Rechts) and also an institution of the State of North Rhine-Westphalia. It is represented by its Rector, Prof. Dr. Susanne Menzel-Riedl.

    Supervisory authority:
    Ministerium für Kultur und Wissenschaft des Landes Nordrhein-Westfalen
    Völklinger Straße 49
    40221 Düsseldorf, Germany

    VAT ID: DE 126118759

    Responsible for content pursuant to § 18 (2) MStV:
    The Dean of the Faculty of Medicine
    Prof. Dr. Frank Ulrich Müller
    Albert-Schweitzer-Campus 1, Building D3
    48149 Münster, Germany
    Phone: +49 251 83 52263
    Fax: +49 251 83 55004
    Email: dekanmed@ukmuenster.de


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