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SQN Submission File Genome Feature Table
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 |
| 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. |
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The exact identification of plastid or mitochondrial genomes is very tricky. To help you to identify possible organelle genomes, we provide you a table that gives you some indications which scaffolds may contain organelle scaffolds. The highest lines are probably organelle scaffolds. Depending on your selected tools the table contains more or fewer columns. The option for "Scan for organelles" will perform searches against our local plastid and mitochondrial gene database. Plastid scaffolds usually comprise between 4 and 25 kbp. While mitochondrial scaffolds cover 1 to 200 kbp for protists, 11 to 28 kbp in animals and 19 to 1000 kbp in plants and fungi. We are using partially filtered data for the analysis to get as many indications as possible. You can verify your results by searching the whole scaffold against the NCBI nucleotide database. You can click on a scaffold and submit the scaffold directly to NCBI MegaBlast.
tRNA: number of tRNAs. rRNA: number of rRNAs. rRNA(p): number of partial rRNAs (different codons). Mitos: number of matches against our mitochondrial gene database. Plastids: number of matches against our plastid gene database. GC dev: deviation of the GC content compared to the average. Len [kbp]: scaffold length in kilobase pairs. MD: mitochondrial gene matches per 10 kilobase pairs. PD: plastid gene matches per 10 kilobase pairs. Score: rough scoring to estimate the organelles.
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.
