v.1.2.4

Job c9baedb1 - CrBVI

Status
Finished
Finished at
2021/02/03 20:12
Run time
3.43 min
Mail notification:
roman.martin@uni-marburg.de
Notification date:
2021/04/01 16:09

Results

Your genome annotation results are ready and at least available until 2021/16/03 20:12.

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. doi: 10.1093/bioinformatics/btaa1003.

Scaffold Repeats Gene tRNA Total
Total 4871 7592 44 12507
VLTN01000001.1 172 304 0 476
VLTN01000002.1 131 292 0 423
VLTN01000003.1 119 282 0 401
VLTN01000004.1 71 254 3 328
VLTN01000005.1 104 207 0 311
VLTN01000006.1 120 187 1 308
VLTN01000007.1 74 162 0 236
VLTN01000008.1 76 122 1 199
VLTN01000009.1 121 127 3 251
VLTN01000010.1 97 147 0 244
VLTN01000011.1 111 115 0 226
VLTN01000012.1 89 144 0 233
VLTN01000013.1 95 154 0 249
VLTN01000014.1 80 130 1 211
VLTN01000015.1 63 153 0 216
VLTN01000016.1 55 158 4 217
VLTN01000017.1 121 125 2 248
VLTN01000018.1 52 150 1 203
VLTN01000019.1 58 136 0 194
VLTN01000020.1 77 127 0 204
VLTN01000021.1 72 134 0 206
VLTN01000022.1 84 78 0 162
VLTN01000023.1 49 116 0 165
VLTN01000024.1 36 112 0 148
VLTN01000025.1 58 79 1 138
VLTN01000026.1 58 96 1 155
VLTN01000027.1 48 110 9 167
VLTN01000028.1 62 88 0 150
VLTN01000029.1 99 56 1 156
VLTN01000030.1 75 82 0 157
VLTN01000031.1 83 77 0 160
VLTN01000032.1 48 91 0 139
VLTN01000033.1 51 93 0 144
VLTN01000034.1 67 65 0 132
VLTN01000035.1 33 96 0 129
VLTN01000036.1 50 77 0 127
VLTN01000037.1 49 75 0 124
VLTN01000038.1 64 60 0 124
VLTN01000039.1 48 69 0 117
VLTN01000040.1 30 79 0 109
VLTN01000041.1 33 74 0 107
VLTN01000042.1 42 62 0 104
VLTN01000043.1 49 57 0 106
VLTN01000044.1 33 50 0 83
VLTN01000045.1 40 74 0 114
VLTN01000046.1 45 80 0 125
VLTN01000047.1 10 78 8 96
VLTN01000048.1 33 68 0 101
VLTN01000049.1 54 51 0 105
VLTN01000050.1 45 69 0 114
VLTN01000051.1 48 31 0 79
VLTN01000052.1 37 44 0 81
VLTN01000053.1 29 63 0 92
VLTN01000054.1 20 62 0 82
VLTN01000055.1 40 35 0 75
VLTN01000056.1 38 51 0 89
VLTN01000057.1 38 47 0 85
VLTN01000058.1 20 63 0 83
VLTN01000059.1 31 47 0 78
VLTN01000060.1 25 49 0 74
VLTN01000061.1 27 45 0 72
VLTN01000062.1 45 30 0 75
VLTN01000063.1 29 44 0 73
VLTN01000064.1 27 28 0 55
VLTN01000065.1 20 39 0 59
VLTN01000066.1 36 40 0 76
VLTN01000067.1 12 32 2 46
VLTN01000068.1 22 50 0 72
VLTN01000069.1 53 29 0 82
VLTN01000070.1 37 37 0 74
VLTN01000071.1 31 47 0 78
VLTN01000072.1 19 47 0 66
VLTN01000073.1 32 65 0 97
VLTN01000074.1 19 24 0 43
VLTN01000075.1 33 25 0 58
VLTN01000076.1 21 32 0 53
VLTN01000077.1 21 44 0 65
VLTN01000078.1 22 19 0 41
VLTN01000079.1 39 20 0 59
VLTN01000080.1 16 14 3 33
VLTN01000081.1 12 31 0 43
VLTN01000082.1 26 34 0 60
VLTN01000083.1 38 20 0 58
VLTN01000084.1 14 26 0 40
VLTN01000085.1 42 12 0 54
VLTN01000086.1 14 14 0 28
VLTN01000087.1 7 13 0 20
VLTN01000088.1 13 12 0 25
VLTN01000089.1 15 13 0 28
VLTN01000090.1 27 12 0 39
VLTN01000091.1 31 11 0 42
VLTN01000092.1 10 21 0 31
VLTN01000093.1 4 24 0 28
VLTN01000094.1 13 6 0 19
VLTN01000095.1 2 12 0 14
VLTN01000096.1 9 5 0 14
VLTN01000097.1 1 13 0 14
VLTN01000098.1 6 17 0 23
VLTN01000099.1 12 13 0 25
VLTN01000100.1 1 5 0 6
VLTN01000101.1 22 8 1 31
VLTN01000102.1 0 6 0 6
VLTN01000103.1 3 6 0 9
VLTN01000104.1 4 8 0 12
VLTN01000105.1 4 13 0 17
VLTN01000106.1 3 5 0 8
VLTN01000107.1 22 4 0 26
VLTN01000108.1 2 10 0 12
VLTN01000109.1 10 4 0 14
VLTN01000110.1 5 4 0 9
VLTN01000111.1 8 2 0 10
VLTN01000112.1 1 6 0 7
VLTN01000113.1 4 5 0 9
VLTN01000114.1 10 5 0 15
VLTN01000115.1 1 2 0 3
VLTN01000116.1 6 0 0 6
VLTN01000117.1 24 1 0 25
VLTN01000118.1 2 3 0 5
VLTN01000119.1 1 0 0 1
VLTN01000120.1 2 1 0 3
VLTN01000121.1 0 2 0 2
VLTN01000122.1 0 4 0 4
VLTN01000123.1 3 6 0 9
VLTN01000124.1 1 0 0 1
VLTN01000125.1 9 3 0 12
VLTN01000126.1 9 2 0 11
VLTN01000127.1 1 2 0 3
VLTN01000128.1 10 4 0 14
VLTN01000129.1 2 4 0 6
VLTN01000130.1 3 4 0 7
VLTN01000131.1 5 1 0 6
VLTN01000132.1 9 1 0 10
VLTN01000133.1 3 4 0 7
VLTN01000134.1 2 2 0 4
VLTN01000135.1 2 3 0 5
VLTN01000136.1 1 2 0 3
VLTN01000137.1 5 2 0 7
VLTN01000138.1 1 3 0 4
VLTN01000139.1 7 3 0 10
VLTN01000140.1 2 2 0 4
VLTN01000141.1 0 3 0 3
VLTN01000142.1 0 5 0 5
VLTN01000143.1 2 4 0 6
VLTN01000144.1 0 1 0 1
VLTN01000145.1 0 4 0 4
VLTN01000146.1 0 5 0 5
VLTN01000147.1 5 3 0 8
VLTN01000148.1 10 0 0 10
VLTN01000149.1 0 4 0 4
VLTN01000151.1 1 2 0 3
VLTN01000152.1 3 1 0 4
VLTN01000154.1 1 4 0 5
VLTN01000155.1 8 3 0 11
VLTN01000156.1 1 0 0 1
VLTN01000159.1 1 3 0 4
VLTN01000160.1 0 2 0 2
VLTN01000161.1 0 1 0 1
VLTN01000162.1 1 2 0 3
VLTN01000163.1 1 0 0 1
VLTN01000164.1 0 1 0 1
VLTN01000165.1 8 2 0 10
VLTN01000166.1 0 2 0 2
VLTN01000167.1 1 2 0 3
VLTN01000168.1 1 1 0 2
VLTN01000169.1 0 1 0 1
CM017891.1 0 0 2 2

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

Prediction outputs
Genome Annotation GFF Feature Table Writing Organelle Scan Mitos Plastids WindowMasker Import RepeatMasker Import RepeatMasker Results RepeatMasker Stats tRNAscan-SE 2 Import tRNAscan-SE 2 Results Barrnap Import Barrnap Results SILVA LSU Import SILVA LSU Results BRAKER Import Swiss-Prot Database Results EggNog 5 Database Results

What to cite
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.
Smit AFA. RepeatMasker. <a target="_blank" href="http://www.repeatmasker.org">URL</a>.
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
Stanke M, Diekhans M, Baertsch, R. and Haussler D (2008). Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics.
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.
Hoff KJ, Lomsadze A, Borodovsky M, Stanke M (2019). Whole-Genome Annotation with BRAKER. Methods Mol Biol. 1962:65-95.
Martin R, Hackl T, Hattab G, Fischer MG, Heider D (2020). MOSGA: Modular Open-Source Genome Annotator. Bioinformatics. doi: 10.1093/bioinformatics/btaa1003
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.
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
Langmead B, Salzberg SL (2012). Fast gapped-read alignment with Bowtie 2. Nat Methods. 4;9(4):357-9. doi: 10.1038/nmeth.1923
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.
Seemann T. barrnap 0.9 : rapid ribosomal RNA prediction. https://github.com/tseemann/barrnap
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.
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.
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.
Morgulis A, Gertz EM, Schäffer AA, Agarwala R (2006). WindowMasker: window-based masker for sequenced genomes. Bioinformatics. 22(2):134‐141.
Bairoch, A., Boeckmann, B., Ferro, S., and Gasteiger, E. (2004). Swiss-Prot: juggling between evolution and stability. Briefings in Bioinformatics ,5(1), 39–55.
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
Hoff, K. J. and Stanke, M. (2019). Predicting Genes in Single Genomes with AUGUSTUS. Current Protocols in Bioinformatics, 65(1).
Buchfink B, Xie C, Huson DH (2015). Fast and sensitive protein alignment using DIAMOND. Nat Methods. 12(1):59‐60.





Upload your assembled FASTA genome file.

Priority (highest priority first)

    Functional Enrichment Analysis


    Protein-Protein Interactions Analysis


    Protein-Protein Interactions Analysis


    Choose your prediction tools

    Genes

    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

    Detection of repeating sequences.

    tRNAs

    Prediction of tRNA sequences.

    rRNAs

    Search for rRNA sequence matches.


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    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).

    Please take care about the licenses of the selected tools.

    Whenever you use MOSGA please cite us:
    Roman Martin, Thomas Hackl, Georges Hattab, Matthias Fischer, Dominik Heider (2020). MOSGA: Modular Open-Source Genome Annotator. Bioinformatics. 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.