v.2.1.5

Job ab9d6fa8 - CrBVI

Status
Finished
Finished at
2021/02/03 15:36
Finished in
3 min
Mail notification:
roman.martin@uni-marburg.de
Notification date:
2020/21/07 14:14

Annotation results

Your genome annotation results are ready and at least available until 2021/09/03 15:36.

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.
  • 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.

Scaffold Repeats Gene tRNA Total
Total 4546 7826 192 12564
scaffold_1 170 315 31 516
scaffold_2 120 298 1 419
scaffold_3 109 289 0 398
scaffold_4 66 260 7 333
scaffold_5 94 213 0 307
scaffold_6 106 195 8 309
scaffold_7 78 165 4 247
scaffold_8 60 132 1 193
scaffold_9 113 135 14 262
scaffold_10 93 152 5 250
scaffold_11 108 116 1 225
scaffold_12 75 149 1 225
scaffold_13 84 161 0 245
scaffold_14 74 134 3 211
scaffold_15 69 162 5 236
scaffold_16 49 157 11 217
scaffold_17 116 131 2 249
scaffold_18 45 152 4 201
scaffold_19 58 133 0 191
scaffold_20 69 129 0 198
scaffold_21 77 137 0 214
scaffold_22 86 80 0 166
scaffold_23 44 112 0 156
scaffold_24 38 116 0 154
scaffold_25 56 81 1 138
scaffold_26 53 101 1 155
scaffold_27 43 115 9 167
scaffold_28 62 88 8 158
scaffold_29 89 60 1 150
scaffold_30 62 86 0 148
scaffold_31 82 75 0 157
scaffold_32 51 94 0 145
scaffold_33 42 94 0 136
scaffold_34 68 63 3 134
scaffold_35 31 93 6 130
scaffold_36 46 85 0 131
scaffold_37 43 76 0 119
scaffold_38 55 63 0 118
scaffold_39 48 70 0 118
scaffold_40 29 78 0 107
scaffold_41 29 72 2 103
scaffold_42 36 60 0 96
scaffold_43 43 61 0 104
scaffold_44 30 53 0 83
scaffold_45 36 76 0 112
scaffold_46 38 82 1 121
scaffold_47 10 76 8 94
scaffold_48 35 68 0 103
scaffold_49 52 52 0 104
scaffold_50 43 69 0 112
scaffold_51 54 29 0 83
scaffold_52 27 50 0 77
scaffold_53 25 65 0 90
scaffold_54 16 65 8 89
scaffold_55 42 36 2 80
scaffold_56 31 57 0 88
scaffold_57 23 49 0 72
scaffold_58 17 66 0 83
scaffold_59 33 49 0 82
scaffold_60 17 53 0 70
scaffold_61 26 51 0 77
scaffold_62 30 32 1 63
scaffold_63 26 44 2 72
scaffold_64 25 26 0 51
scaffold_65 17 41 0 58
scaffold_66 32 42 5 79
scaffold_67 11 33 2 46
scaffold_68 21 49 0 70
scaffold_69 53 30 0 83
scaffold_70 32 40 0 72
scaffold_71 28 48 0 76
scaffold_72 14 48 0 62
scaffold_73 29 66 0 95
scaffold_74 27 24 1 52
scaffold_75 25 26 0 51
scaffold_76 31 34 1 66
scaffold_77 17 46 0 63
scaffold_78 16 21 0 37
scaffold_79 34 18 0 52
scaffold_80 12 15 3 30
scaffold_81 10 29 0 39
scaffold_82 25 35 0 60
scaffold_83 33 24 0 57
scaffold_84 12 26 0 38
scaffold_85 40 13 0 53
scaffold_86 11 15 0 26
scaffold_87 8 14 0 22
scaffold_88 15 12 0 27
scaffold_89 14 14 0 28
scaffold_90 24 10 0 34
scaffold_91 30 10 0 40
scaffold_92 9 21 0 30
scaffold_93 6 25 0 31
scaffold_94 15 8 0 23
scaffold_95 1 13 0 14
scaffold_96 9 7 0 16
scaffold_97 1 15 3 19
scaffold_98 5 18 1 24
scaffold_99 12 14 0 26
scaffold_100 3 6 0 9
scaffold_101 16 9 1 26
scaffold_102 0 8 0 8
scaffold_103 2 7 0 9
scaffold_104 4 9 0 13
scaffold_105 3 14 0 17
scaffold_106 3 5 0 8
scaffold_107 22 7 0 29
scaffold_108 2 10 0 12
scaffold_109 10 5 0 15
scaffold_110 6 7 5 18
scaffold_111 10 4 0 14
scaffold_112 1 6 0 7
scaffold_113 4 5 0 9
scaffold_114 10 5 0 15
scaffold_116 6 0 0 6
scaffold_117 24 1 0 25
scaffold_118 2 5 0 7
scaffold_119 1 0 0 1
scaffold_120 8 2 0 10
scaffold_122 0 4 0 4
scaffold_123 2 6 0 8
scaffold_124 9 1 0 10
scaffold_125 9 3 0 12
scaffold_126 8 3 0 11
scaffold_127 1 3 0 4
scaffold_128 10 4 0 14
scaffold_129 2 4 0 6
scaffold_130 3 2 0 5
scaffold_131 5 0 0 5
scaffold_132 9 1 0 10
scaffold_133 3 3 0 6
scaffold_134 2 2 0 4
scaffold_135 2 4 0 6
scaffold_136 2 2 0 4
scaffold_137 5 4 0 9
scaffold_138 1 3 0 4
scaffold_139 8 3 0 11
scaffold_140 1 2 0 3
scaffold_142 0 6 0 6
scaffold_143 2 4 0 6
scaffold_147 2 3 0 5
scaffold_148 10 0 0 10
scaffold_151 2 3 0 5
scaffold_152 1 1 0 2
scaffold_154 1 4 0 5
scaffold_155 8 3 0 11
scaffold_156 1 0 0 1
scaffold_157 1 1 0 2
scaffold_159 1 3 0 4
scaffold_162 4 4 0 8
scaffold_163 1 1 0 2
scaffold_165 8 2 0 10
scaffold_167 1 2 0 3
scaffold_149 0 4 0 4
scaffold_160 0 2 0 2
scaffold_145 0 4 0 4
scaffold_164 0 1 0 1
scaffold_141 0 3 0 3
scaffold_121 0 2 0 2
scaffold_150 0 2 0 2
scaffold_168 0 1 0 1
scaffold_158 0 1 0 1
scaffold_115 0 2 0 2
scaffold_161 0 1 0 1
scaffold_146 0 4 0 4
scaffold_169 0 1 0 1
scaffold_166 0 1 0 1
scaffold_144 0 1 0 1
scaffold_170 0 0 19 19

Annotation database Snakemake configuration Snakemake log Validation File Error Summary Discrepancy Report What to cite

Single outputs
Genome Annotation GFF Feature Table Writing Organelle Scan WindowMasker Import tRNAscan-SE 2 Import tRNAscan-SE 2 Results SILVA LSU Import SILVA LSU Results Swiss-Prot Database Results EggNog 5 Database Results

What to cite
Kim D, Langmead B, Salzberg SL (2015). HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 12(4):357-60. doi: 10.1038/nmeth.3317
Brůna, T., Hoff, K.J., Lomsadze, A., Stanke, M., & Borodovsky, M. (2020). BRAKER2: Automatic Eukaryotic Genome Annotation with GeneMark-EP+ and AUGUSTUS Supported by a Protein Database, NAR Genomics and Bioinformatics 3(1):lqaa108, doi: 10.1093/nargab/lqaa108.
Stanke M, Diekhans M, Baertsch, R. and Haussler D (2008). Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics.
Hoff KJ, Lomsadze A, Borodovsky M, Stanke M (2019). Whole-Genome Annotation with BRAKER. Methods Mol Biol. 1962:65-95.
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO (2013). The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41 (D1): D590-D596.
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.
Bairoch, A., Boeckmann, B., Ferro, S., and Gasteiger, E. (2004). Swiss-Prot: juggling between evolution and stability. Briefings in Bioinformatics ,5(1), 39–55.
Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, Mende DR, Letunic I, Rattei T, Jensen LJ, Von Mering C, Bork P (2019). eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 47.
Langmead B, Salzberg SL (2012). Fast gapped-read alignment with Bowtie 2. Nat Methods. 4;9(4):357-9. doi: 10.1038/nmeth.1923
Martin R, Dreßler H, Hattab G, Hackl T, Fischer MG, Heider D (2021). MOSGA 2: Comparative genomics and validation tools. bioRxiv 2021.07.29.454382. doi: 10.1101/2021.07.29.454382
Stanke M, Schöffmann O, Morgenstern, B, Waack S (2006). Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics 7, 62.
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
Hoff, K. J. and Stanke, M. (2019). Predicting Genes in Single Genomes with AUGUSTUS. Current Protocols in Bioinformatics, 65(1).
Martin R, Hackl T, Hattab G, Fischer MG, Heider D (2020). MOSGA: Modular Open-Source Genome Annotator. Bioinformatics. 36(22-23):5514-5515. doi: 10.1093/bioinformatics/btaa1003
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009). 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. A 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352
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
Hoff KJ, Lange S, Lomsadze A, Borodovsky M, Stanke M (2016). BRAKER1: unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS. Bioinformatics, 32(5):767-769.
Morgulis A, Gertz EM, Schäffer AA, Agarwala R (2006). WindowMasker: window-based masker for sequenced genomes. Bioinformatics. 22(2):134‐141.
Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ, Von Mering C, Bork P (2017). Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper. Mol Biol Evol.

Upload your assembled FASTA eukaryotic genome file.

Priority (highest priority first)

    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.

    Assembly Validation

    Genome Completeness

    Validate genome completeness.

    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.

    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 Philipps University of Marburg hosts this MOSGA instance for demonstration purposes. It runs on an AMD Zen processor with 16 threads and 32 GB of memory.

    We preserve the last 100 job submissions online until that limit exceeds. After that, we delete the oldest submission job that is at least more aged than 14 days. Incoming jobs are queued and processed as soon as possible. Computation tasks that stress our hardware longer than 48 hours could be terminated. We recommend not to upload files that are larger than 2 GiB.

    We reserve the right to analyze failed jobs to determine errors and 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 if your job failed to avoid or fix the issue.


    Server usage