v.2.0.5

Job 9237305b

Status
Finished
Finished at
2021/11/08 20:01
Run time
118.08 min

Annotation results

Your genome annotation results are ready and at least available until 2021/25/08 20:01.

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. bioRxiv 2021.07.29.454382. doi: 10.1101/2021.07.29.454382.

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 5474 9639 44 15157
VLTN01000001.1 147 412 0 559
VLTN01000002.1 137 353 0 490
VLTN01000003.1 130 351 0 481
VLTN01000004.1 99 284 3 386
VLTN01000005.1 100 251 0 351
VLTN01000006.1 111 218 1 330
VLTN01000007.1 98 224 0 322
VLTN01000008.1 81 162 1 244
VLTN01000009.1 96 171 3 270
VLTN01000010.1 104 173 0 277
VLTN01000011.1 77 168 0 245
VLTN01000012.1 77 216 0 293
VLTN01000013.1 72 186 0 258
VLTN01000014.1 107 156 1 264
VLTN01000015.1 71 187 0 258
VLTN01000016.1 71 183 4 258
VLTN01000017.1 92 170 2 264
VLTN01000018.1 74 179 1 254
VLTN01000019.1 85 147 0 232
VLTN01000020.1 73 171 0 244
VLTN01000021.1 78 157 0 235
VLTN01000022.1 92 126 0 218
VLTN01000023.1 51 152 0 203
VLTN01000024.1 73 132 0 205
VLTN01000025.1 60 99 1 160
VLTN01000026.1 48 121 1 170
VLTN01000027.1 49 130 9 188
VLTN01000028.1 72 107 0 179
VLTN01000029.1 117 85 1 203
VLTN01000030.1 81 128 0 209
VLTN01000031.1 68 109 0 177
VLTN01000032.1 68 107 0 175
VLTN01000033.1 58 124 0 182
VLTN01000034.1 71 100 0 171
VLTN01000035.1 40 122 0 162
VLTN01000036.1 71 103 0 174
VLTN01000037.1 27 85 0 112
VLTN01000038.1 77 104 0 181
VLTN01000039.1 61 87 0 148
VLTN01000040.1 47 93 0 140
VLTN01000041.1 32 94 0 126
VLTN01000042.1 51 83 0 134
VLTN01000043.1 52 67 0 119
VLTN01000044.1 60 82 0 142
VLTN01000045.1 53 86 0 139
VLTN01000046.1 56 99 0 155
VLTN01000047.1 13 88 8 109
VLTN01000048.1 36 78 0 114
VLTN01000049.1 39 70 0 109
VLTN01000050.1 30 87 0 117
VLTN01000051.1 112 45 0 157
VLTN01000052.1 38 58 0 96
VLTN01000053.1 35 82 0 117
VLTN01000054.1 23 75 0 98
VLTN01000055.1 40 42 0 82
VLTN01000056.1 50 68 0 118
VLTN01000057.1 43 73 0 116
VLTN01000058.1 44 70 0 114
VLTN01000059.1 27 45 0 72
VLTN01000060.1 34 66 0 100
VLTN01000061.1 35 57 0 92
VLTN01000062.1 52 52 0 104
VLTN01000063.1 40 55 0 95
VLTN01000064.1 36 46 0 82
VLTN01000065.1 18 59 0 77
VLTN01000066.1 24 52 0 76
VLTN01000067.1 20 51 2 73
VLTN01000068.1 13 56 0 69
VLTN01000069.1 31 26 0 57
VLTN01000070.1 31 47 0 78
VLTN01000071.1 27 60 0 87
VLTN01000072.1 33 52 0 85
VLTN01000073.1 39 57 0 96
VLTN01000074.1 40 41 0 81
VLTN01000075.1 44 35 0 79
VLTN01000076.1 22 35 0 57
VLTN01000077.1 15 52 0 67
VLTN01000078.1 46 21 0 67
VLTN01000079.1 34 29 0 63
VLTN01000080.1 16 23 3 42
VLTN01000081.1 20 31 0 51
VLTN01000082.1 23 41 0 64
VLTN01000083.1 24 27 0 51
VLTN01000084.1 11 28 0 39
VLTN01000085.1 28 18 0 46
VLTN01000086.1 27 15 0 42
VLTN01000087.1 10 17 0 27
VLTN01000088.1 41 11 0 52
VLTN01000089.1 24 21 0 45
VLTN01000090.1 17 18 0 35
VLTN01000091.1 22 15 0 37
VLTN01000092.1 14 18 0 32
VLTN01000093.1 12 29 0 41
VLTN01000094.1 19 7 0 26
VLTN01000095.1 16 20 0 36
VLTN01000096.1 8 0 0 8
VLTN01000097.1 3 18 0 21
VLTN01000098.1 2 20 0 22
VLTN01000099.1 15 14 0 29
VLTN01000100.1 10 10 0 20
VLTN01000101.1 22 11 1 34
VLTN01000102.1 2 1 0 3
VLTN01000103.1 12 14 0 26
VLTN01000104.1 13 12 0 25
VLTN01000105.1 11 17 0 28
VLTN01000106.1 4 14 0 18
VLTN01000107.1 4 0 0 4
VLTN01000108.1 4 1 0 5
VLTN01000109.1 10 3 0 13
VLTN01000110.1 11 12 0 23
VLTN01000111.1 12 1 0 13
VLTN01000112.1 7 0 0 7
VLTN01000113.1 11 3 0 14
VLTN01000114.1 4 0 0 4
VLTN01000115.1 6 0 0 6
VLTN01000116.1 12 1 0 13
VLTN01000117.1 2 3 0 5
VLTN01000118.1 5 4 0 9
VLTN01000119.1 6 0 0 6
VLTN01000120.1 5 3 0 8
VLTN01000121.1 7 1 0 8
VLTN01000122.1 5 0 0 5
VLTN01000123.1 4 7 0 11
VLTN01000124.1 0 1 0 1
VLTN01000125.1 3 6 0 9
VLTN01000126.1 6 4 0 10
VLTN01000127.1 9 4 0 13
VLTN01000128.1 1 0 0 1
VLTN01000129.1 14 9 0 23
VLTN01000130.1 13 5 0 18
VLTN01000131.1 12 5 0 17
VLTN01000132.1 2 4 0 6
VLTN01000133.1 9 5 0 14
VLTN01000134.1 9 5 0 14
VLTN01000135.1 7 10 0 17
VLTN01000136.1 10 5 0 15
VLTN01000137.1 3 5 0 8
VLTN01000138.1 8 3 0 11
VLTN01000139.1 8 3 0 11
VLTN01000140.1 8 2 0 10
VLTN01000141.1 8 4 0 12
VLTN01000142.1 5 5 0 10
VLTN01000143.1 6 5 0 11
VLTN01000144.1 5 0 0 5
VLTN01000145.1 2 5 0 7
VLTN01000146.1 6 2 0 8
VLTN01000147.1 3 0 0 3
VLTN01000148.1 9 2 0 11
VLTN01000149.1 7 2 0 9
VLTN01000150.1 4 1 0 5
VLTN01000151.1 4 4 0 8
VLTN01000152.1 11 3 0 14
VLTN01000153.1 4 3 0 7
VLTN01000154.1 5 8 0 13
VLTN01000155.1 3 2 0 5
VLTN01000156.1 4 0 0 4
VLTN01000157.1 5 2 0 7
VLTN01000158.1 4 0 0 4
VLTN01000159.1 5 2 0 7
VLTN01000160.1 4 4 0 8
VLTN01000161.1 6 4 0 10
VLTN01000162.1 5 0 0 5
VLTN01000163.1 3 3 0 6
VLTN01000164.1 2 2 0 4
VLTN01000165.1 4 7 0 11
VLTN01000166.1 1 4 0 5
VLTN01000167.1 1 2 0 3
VLTN01000168.1 2 4 0 6
VLTN01000169.1 4 0 0 4
CM017891.1 0 0 2 2

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

Single outputs
Genome Annotation GFF Organelle Scan Mitos Plastids Red Import Red Results 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
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
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., 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.
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.
Seemann T. barrnap 0.9 : rapid ribosomal RNA prediction. https://github.com/tseemann/barrnap
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
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
Bairoch, A., Boeckmann, B., Ferro, S., and Gasteiger, E. (2004). Swiss-Prot: juggling between evolution and stability. Briefings in Bioinformatics ,5(1), 39–55.
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
Girgis HZ (2015). Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale. BMC Bioinformatics 16:227. doi: 10.1186/s12859-015-0654-5



Log Viewer





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
    9237305b CrBVI.fa 2021/11/08 18:02 2021/11/08 18:03 2021/11/08 20:01 Annotation Finished
    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.

    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. bioRxiv 2021.07.29.454382. doi: 10.1101/2021.07.29.454382.

    Server usage