02f874e

Job ec6d1246

Status
Finished
Finished at
2021/07/07 15:05
Run time
1.12 min

Annotation results

Your genome annotation results are ready and at least available until 2021/21/07 15:05.

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

SQN Submission File 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.

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


Scaffold Repeats Gene tRNA Total
Total 419 1254 7 1680
ptK-f1a_50 22 74 0 96
ptK-f1a_51 13 97 0 110
ptK-f1a_52 20 74 0 94
ptK-f1a_53 5 64 0 69
ptK-f1a_54 3 54 0 57
ptK-f1a_55 6 39 0 45
ptK-f1a_56 13 40 0 53
ptK-f1a_57 0 33 0 33
ptK-f1a_58 0 54 0 54
ptK-f1a_59 0 48 1 49
ptK-f1a_60 1 29 3 33
ptK-f1a_61 7 44 0 51
ptK-f1a_62 0 32 0 32
ptK-f1a_63 0 15 0 15
ptK-f1a_64 10 38 0 48
ptK-f1a_65 0 36 0 36
ptK-f1a_66 8 17 0 25
ptK-f1a_67 0 32 0 32
ptK-f1a_68 0 39 0 39
ptK-f1a_69 23 30 0 53
ptK-f1a_70 15 28 0 43
ptK-f1a_71 0 28 0 28
ptK-f1a_72 5 29 0 34
ptK-f1a_73 0 31 0 31
ptK-f1a_74 18 26 1 45
ptK-f1a_75 12 13 0 25
ptK-f1a_76 29 19 0 48
ptK-f1a_77 0 18 0 18
ptK-f1a_78 7 16 0 23
ptK-f1a_79 18 6 0 24
ptK-f1a_80 0 0 2 2
ptK-f1a_81 0 10 0 10
ptK-f1a_82 9 12 0 21
ptK-f1a_83 6 10 0 16
ptK-f1a_84 22 4 0 26
ptK-f1a_85 0 5 0 5
ptK-f1a_86 14 11 0 25
ptK-f1a_87 0 4 0 4
ptK-f1a_88 11 8 0 19
ptK-f1a_89 0 1 0 1
ptK-f1a_90 1 6 0 7
ptK-f1a_91 0 4 0 4
ptK-f1a_92 14 3 0 17
ptK-f1a_93 0 3 0 3
ptK-f1a_94 12 3 0 15
ptK-f1a_95 9 9 0 18
ptK-f1a_96 4 7 0 11
ptK-f1a_97 16 2 0 18
ptK-f1a_98 0 7 0 7
ptK-f1a_99 8 2 0 10
ptK-f1a_100 14 2 0 16
ptK-f1a_101 7 6 0 13
ptK-f1a_102 4 3 0 7
ptK-f1a_103 1 3 0 4
ptK-f1a_104 0 1 0 1
ptK-f1a_105 0 2 0 2
ptK-f1a_106 11 2 0 13
ptK-f1a_107 0 2 0 2
ptK-f1a_108 5 1 0 6
ptK-f1a_109 0 5 0 5
ptK-f1a_110 0 4 0 4
ptK-f1a_111 12 1 0 13
ptK-f1a_112 0 3 0 3
ptK-f1a_113 0 1 0 1
ptK-f1a_114 2 1 0 3
ptK-f1a_115 0 1 0 1
ptK-f1a_116 2 1 0 3
ptK-f1a_117 0 1 0 1

Taxonomy search result
Tool Hit NCBI-ID Distance
Augustus Vitrella_brassicaformis 1169539 7
BUSCO eukaryota_odb10 2759 4
Validation File Error Summary Discrepancy Report Annotation database Snakemake configuration Snakemake log Taxonomy Search What to cite

Outputs and logs
Genome Annotation GFF Feature Table Writing Organelle Scan Mitos Plastids WindowMasker Import tRNAscan-SE 2 Import tRNAscan-SE 2 Results Barrnap Import Barrnap Results Augustus Import Swiss-Prot Database Results BUSCO Summary BUSCO Graph BUSCO Matches VecScreen Report VecScreen UniVec Raw Matches VecScreen UniVec Matches

What to cite
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
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
Stanke. M., Schöffmann, O., Morgenstern, B. and Waack, S. (2006). Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics 7, 62.
Bairoch, A., Boeckmann, B., Ferro, S., and Gasteiger, E. (2004). Swiss-Prot: juggling between evolution and stability. Briefings in Bioinformatics ,5(1), 39–55.
Morgulis A, Gertz EM, Schäffer AA, Agarwala R (2006). WindowMasker: window-based masker for sequenced genomes. Bioinformatics. 22(2):134‐141.
Seemann T. barrnap 0.9 : rapid ribosomal RNA prediction. https://github.com/tseemann/barrnap
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
Buchfink B, Xie C, Huson DH (2015). Fast and sensitive protein alignment using DIAMOND. Nat Methods. 12(1):59‐60.
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
Stanke, M., Diekhans, M., Baertsch, R. and Haussler, D. (2008). Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics, doi: 10.1093/bioinformatics/btn013.







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
    60b5f985 Branchiostoma floridae pipeline 2021/12/07 19:10 2021/12/07 19:11 2021/23/07 00:31 Annotation Failed
    ec6d1246 ptk.fa 2021/07/07 14:11 2021/07/07 15:04 2021/07/07 15:05 Annotation Finished

    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.

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