Version: v.1.1.9

Job c9baedb1 - CrBVI

Status
Finished
Finished at
2021/05/01 11:27
Run time
44.05 min
Mail notification:
roman.martin@uni-marburg.de
Notification date:
2021/04/01 17:09

Results

Your genome annotation results are ready and at least available until 2021/19/01 11:27.

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 rRNA Total
Total 4688 8694 44 6 13432
VLTN01000001.1 164 362 0 0 526
VLTN01000002.1 124 325 0 0 449
VLTN01000003.1 113 323 0 0 436
VLTN01000004.1 67 275 3 0 345
VLTN01000005.1 104 226 0 0 330
VLTN01000006.1 120 203 1 0 324
VLTN01000007.1 70 190 0 0 260
VLTN01000008.1 70 143 1 0 214
VLTN01000009.1 116 147 3 0 266
VLTN01000010.1 94 161 0 0 255
VLTN01000011.1 111 135 0 4 250
VLTN01000012.1 85 164 0 0 249
VLTN01000013.1 93 171 0 0 264
VLTN01000014.1 77 148 1 0 226
VLTN01000015.1 53 175 0 0 228
VLTN01000016.1 55 176 4 0 235
VLTN01000017.1 117 140 2 0 259
VLTN01000018.1 50 162 1 0 213
VLTN01000019.1 57 148 0 0 205
VLTN01000020.1 76 143 0 0 219
VLTN01000021.1 71 145 0 0 216
VLTN01000022.1 79 93 0 0 172
VLTN01000023.1 48 129 0 0 177
VLTN01000024.1 36 123 0 0 159
VLTN01000025.1 57 96 1 0 154
VLTN01000026.1 55 110 1 0 166
VLTN01000027.1 47 118 9 0 174
VLTN01000028.1 61 102 0 0 163
VLTN01000029.1 99 76 1 0 176
VLTN01000030.1 72 94 0 0 166
VLTN01000031.1 75 86 0 0 161
VLTN01000032.1 47 99 0 0 146
VLTN01000033.1 49 103 0 0 152
VLTN01000034.1 62 74 0 0 136
VLTN01000035.1 31 101 0 0 132
VLTN01000036.1 50 92 0 0 142
VLTN01000037.1 42 82 0 0 124
VLTN01000038.1 63 73 0 0 136
VLTN01000039.1 46 76 0 0 122
VLTN01000040.1 24 89 0 0 113
VLTN01000041.1 33 82 0 0 115
VLTN01000042.1 41 74 0 0 115
VLTN01000043.1 49 71 0 0 120
VLTN01000044.1 32 68 0 0 100
VLTN01000045.1 39 84 0 0 123
VLTN01000046.1 45 88 0 0 133
VLTN01000047.1 10 85 8 0 103
VLTN01000048.1 33 76 0 0 109
VLTN01000049.1 52 58 0 0 110
VLTN01000050.1 41 77 0 0 118
VLTN01000051.1 48 36 0 0 84
VLTN01000052.1 38 59 0 0 97
VLTN01000053.1 24 73 0 0 97
VLTN01000054.1 18 74 0 0 92
VLTN01000055.1 37 43 0 0 80
VLTN01000056.1 37 57 0 0 94
VLTN01000057.1 36 60 0 0 96
VLTN01000058.1 19 72 0 0 91
VLTN01000059.1 33 50 0 0 83
VLTN01000060.1 25 55 0 0 80
VLTN01000061.1 30 54 0 0 84
VLTN01000062.1 44 37 0 0 81
VLTN01000063.1 23 51 0 0 74
VLTN01000064.1 27 33 0 0 60
VLTN01000065.1 20 49 0 0 69
VLTN01000066.1 36 45 0 0 81
VLTN01000067.1 10 40 2 0 52
VLTN01000068.1 22 54 0 0 76
VLTN01000069.1 53 34 0 0 87
VLTN01000070.1 36 47 0 0 83
VLTN01000071.1 31 49 0 0 80
VLTN01000072.1 19 53 0 0 72
VLTN01000073.1 30 68 0 0 98
VLTN01000074.1 18 30 0 0 48
VLTN01000075.1 31 30 0 0 61
VLTN01000076.1 21 35 0 0 56
VLTN01000077.1 21 52 0 0 73
VLTN01000078.1 14 22 0 0 36
VLTN01000079.1 39 24 0 0 63
VLTN01000080.1 16 19 3 0 38
VLTN01000081.1 12 33 0 0 45
VLTN01000082.1 24 37 0 0 61
VLTN01000083.1 38 28 0 0 66
VLTN01000084.1 14 28 0 0 42
VLTN01000085.1 41 15 0 0 56
VLTN01000086.1 14 17 0 0 31
VLTN01000087.1 7 20 0 0 27
VLTN01000088.1 13 15 0 0 28
VLTN01000089.1 15 16 0 0 31
VLTN01000090.1 27 15 0 0 42
VLTN01000091.1 30 15 0 0 45
VLTN01000092.1 10 21 0 0 31
VLTN01000093.1 4 26 0 0 30
VLTN01000094.1 13 7 0 0 20
VLTN01000095.1 2 12 0 0 14
VLTN01000098.1 5 19 0 0 24
VLTN01000100.1 1 7 0 0 8
VLTN01000101.1 22 10 1 0 33
VLTN01000102.1 0 7 0 0 7
VLTN01000103.1 3 8 0 0 11
VLTN01000105.1 4 14 0 0 18
VLTN01000110.1 5 8 0 0 13
VLTN01000113.1 4 6 0 0 10
VLTN01000115.1 1 2 0 0 3
VLTN01000120.1 2 2 0 0 4
VLTN01000123.1 3 6 0 0 9
VLTN01000124.1 1 1 0 0 2
VLTN01000126.1 9 3 0 0 12
VLTN01000130.1 3 5 0 0 8
VLTN01000131.1 5 1 0 0 6
VLTN01000139.1 7 3 0 0 10
VLTN01000140.1 2 2 0 0 4
VLTN01000141.1 0 5 0 0 5
VLTN01000142.1 0 6 0 0 6
VLTN01000147.1 5 3 0 0 8
VLTN01000152.1 3 1 0 0 4
VLTN01000168.1 1 2 0 0 3
VLTN01000096.1 0 7 0 0 7
VLTN01000097.1 1 16 0 0 17
VLTN01000099.1 12 16 0 0 28
VLTN01000104.1 4 11 0 0 15
VLTN01000106.1 3 6 0 0 9
VLTN01000107.1 21 8 0 0 29
VLTN01000108.1 2 10 0 0 12
VLTN01000109.1 10 8 0 0 18
VLTN01000111.1 9 5 0 0 14
VLTN01000112.1 1 6 0 0 7
VLTN01000114.1 10 6 0 0 16
VLTN01000116.1 6 1 0 0 7
VLTN01000117.1 18 3 0 0 21
VLTN01000118.1 2 6 0 0 8
VLTN01000119.1 0 1 0 0 1
VLTN01000122.1 0 4 0 0 4
VLTN01000125.1 9 3 0 0 12
VLTN01000127.1 0 5 0 0 5
VLTN01000128.1 10 4 0 0 14
VLTN01000129.1 2 5 0 0 7
VLTN01000132.1 9 4 0 0 13
VLTN01000133.1 3 5 0 0 8
VLTN01000134.1 2 3 0 0 5
VLTN01000135.1 2 5 0 0 7
VLTN01000136.1 1 4 0 0 5
VLTN01000137.1 5 4 0 0 9
VLTN01000138.1 1 4 0 0 5
VLTN01000143.1 2 5 0 0 7
VLTN01000148.1 10 0 0 0 10
VLTN01000151.1 1 3 0 0 4
VLTN01000154.1 1 4 0 0 5
VLTN01000155.1 8 3 0 0 11
VLTN01000156.1 1 1 0 0 2
VLTN01000157.1 0 3 0 0 3
VLTN01000159.1 1 3 0 0 4
VLTN01000162.1 0 5 0 0 5
VLTN01000163.1 1 1 0 0 2
VLTN01000165.1 8 2 0 0 10
VLTN01000167.1 1 2 0 0 3
VLTN01000121.1 0 2 0 0 2
VLTN01000145.1 0 4 0 0 4
VLTN01000146.1 0 5 0 0 5
VLTN01000164.1 0 1 0 0 1
VLTN01000160.1 0 4 0 0 4
VLTN01000158.1 0 1 0 0 1
VLTN01000150.1 0 1 0 0 1
VLTN01000169.1 0 1 0 0 1
VLTN01000161.1 0 2 0 0 2
VLTN01000149.1 0 6 0 0 6
VLTN01000144.1 0 1 0 0 1
CM017891.1 0 0 2 2 4
VLTN01000166.1 0 2 0 0 2

Validation File Error Summary Descrepancy 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
Seemann T. barrnap 0.9 : rapid ribosomal RNA prediction. https://github.com/tseemann/barrnap
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. Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352
Martin R, Hackl T, Hattab G, Fischer MG, Heider D (2020). MOSGA: Modular Open-Source Genome Annotator. Bioinformatics. 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.
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. Apr 12;17:66. doi: 10.1186/s13059-016-0924-1.
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.
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.
Hoff, K J and Stanke, M (2019). Predicting Genes in Single Genomes with AUGUSTUS. Current Protocols in Bioinformatics, 65(1).
Langmead B, Salzberg SL (2012). Fast gapped-read alignment with Bowtie 2. Nat Methods. Mar 4;9(4):357-9. doi: 10.1038/nmeth.1923
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.
Stanke M, Diekhans M, Baertsch, R. and Haussler D (2008). Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics.
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.
Smit AFA. RepeatMasker. <a target="_blank" href="http://www.repeatmasker.org">URL</a>.
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
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.
Kim D, Langmead B, Salzberg SL (2015). HISAT: a fast spliced aligner with low memory requirements. Nat Methods. Apr;12(4):357-60. doi: 10.1038/nmeth.3317
Bruna, 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, bioRxiv, doi: 10.1101/2020.08.10.245134.
Bairoch, A., Boeckmann, B., Ferro, S., and Gasteiger, E. (2004). Swiss-Prot: juggling between evolution and stability. Briefings in Bioinformatics ,5(1), 39–55.
Hoff KJ, Lomsadze A, Borodovsky M, Stanke M (2019). Whole-Genome Annotation with BRAKER. Methods Mol Biol. 1962:65-95.





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    Gene prediction tool

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    Detection of repeating sequences.

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    Prediction of tRNA sequences.

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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.

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