This workflow is intended to produce a draft consensus Monkeypox virus genome from Oxford Nanopore Technologies Sequencing data.
The rough outline of this workflow:
Consensus is masked ('N') in regions of <20x coverage, deletions are represented as "-" and insertions are in lower case. The consensus will require manual review.
The following tables and figures are derived from the output of fastcat.
The plot below shows coverage of the whole genome. Dots represent single nucleotide polymorphisms called by medaka. Bars represent insertions and deletions called by medaka.
APOBEC3 host enzyme action has been implicated in the mutational process of MPX. As described in this virological.org post by Áine O’Toole & Andrew Rambaut.
Variants with respect to the reference sequence as called by medaka .
| chromosome | start | end | quality | reference | alternate | is_indel | DP | DPS | width | context |
|---|---|---|---|---|---|---|---|---|---|---|
| MT903344.1 | 1271 | 1272 | 40.577 | G | A | False | 94 | 46,48 | 1 | GA>AA |
| MT903344.1 | 2600 | 2601 | 39.894 | G | A | False | 140 | 73,67 | 1 | GA>AA |
| MT903344.1 | 3120 | 3121 | 37.441 | G | A | False | 160 | 84,76 | 1 | GA>AA |
| MT903344.1 | 3531 | 3532 | 37.876 | G | A | False | 144 | 77,67 | 1 | GA>AA |
| MT903344.1 | 3827 | 3828 | 36.170 | C | T | False | 242 | 128,114 | 1 | CA>TA |
| MT903344.1 | 7780 | 7781 | 39.654 | C | T | False | 565 | 276,289 | 1 | CG>TG |
| MT903344.1 | 14009 | 14010 | 46.370 | G | T | False | 153 | 84,69 | 1 | GC>TC |
| MT903344.1 | 15437 | 15438 | 49.867 | G | A | False | 172 | 93,79 | 1 | GA>AA |
| MT903344.1 | 21732 | 21733 | 32.937 | G | A | False | 315 | 154,161 | 1 | GA>AA |
| MT903344.1 | 30376 | 30377 | 43.903 | G | A | False | 232 | 126,106 | 1 | GA>AA |
| MT903344.1 | 31062 | 31063 | 35.748 | G | A | False | 219 | 122,97 | 1 | GA>AA |
| MT903344.1 | 34468 | 34469 | 32.079 | G | A | False | 288 | 150,138 | 1 | GA>AA |
| MT903344.1 | 37211 | 37212 | 24.391 | G | A | False | 223 | 106,117 | 1 | GA>AA |
| MT903344.1 | 38369 | 38370 | 40.017 | G | A | False | 154 | 72,82 | 1 | GA>AA |
| MT903344.1 | 38671 | 38672 | 49.767 | C | T | False | 141 | 63,78 | 1 | CA>TA |
| MT903344.1 | 39148 | 39149 | 45.301 | C | T | False | 185 | 90,95 | 1 | CG>TG |
| MT903344.1 | 52894 | 52895 | 40.979 | G | A | False | 145 | 79,66 | 1 | GA>AA |
| MT903344.1 | 54126 | 54127 | 42.907 | G | A | False | 183 | 94,89 | 1 | GA>AA |
| MT903344.1 | 54644 | 54645 | 43.608 | G | A | False | 181 | 86,95 | 1 | GA>AA |
| MT903344.1 | 64306 | 64307 | 39.403 | G | A | False | 324 | 153,171 | 1 | GA>AA |
| MT903344.1 | 73075 | 73076 | 47.886 | C | T | False | 220 | 121,99 | 1 | CG>TG |
| MT903344.1 | 73248 | 73249 | 40.583 | G | A | False | 203 | 113,90 | 1 | GA>AA |
| MT903344.1 | 74214 | 74215 | 44.487 | G | A | False | 123 | 64,59 | 1 | GA>AA |
| MT903344.1 | 76087 | 76088 | 32.847 | CTT | C | True | 206 | 113,93 | 1 | CT>CT |
| MT903344.1 | 77392 | 77393 | 37.690 | G | A | False | 228 | 131,97 | 1 | GA>AA |
| MT903344.1 | 80849 | 80850 | 14.542 | ATT | A | True | 259 | 127,132 | 1 | AT>AT |
| MT903344.1 | 81284 | 81285 | 33.869 | G | A | False | 231 | 109,122 | 1 | GA>AA |
| MT903344.1 | 82382 | 82383 | 44.561 | C | T | False | 281 | 133,148 | 1 | CG>TG |
| MT903344.1 | 82460 | 82461 | 43.265 | G | A | False | 307 | 145,162 | 1 | GA>AA |
| MT903344.1 | 84596 | 84597 | 33.936 | C | T | False | 342 | 176,166 | 1 | CG>TG |
| MT903344.1 | 89108 | 89109 | 2.808 | TA | T | True | 404 | 194,210 | 1 | TA>TA |
| MT903344.1 | 95043 | 95044 | 43.354 | G | A | False | 157 | 69,88 | 1 | GC>AC |
| MT903344.1 | 106166 | 106167 | 3.435 | TC | T | True | 196 | 91,105 | 1 | TC>TC |
| MT903344.1 | 121124 | 121125 | 8.333 | AT | A | True | 222 | 116,106 | 1 | AT>AT |
| MT903344.1 | 124139 | 124140 | 40.941 | G | A | False | 226 | 100,126 | 1 | GA>AA |
| MT903344.1 | 124683 | 124684 | 47.049 | G | A | False | 185 | 83,102 | 1 | GA>AA |
| MT903344.1 | 128707 | 128708 | 45.266 | C | T | False | 357 | 161,196 | 1 | CG>TG |
| MT903344.1 | 133174 | 133175 | 4.108 | GC | G | True | 265 | 128,137 | 1 | GC>GC |
| MT903344.1 | 133175 | 133176 | 1.383 | CA | C | True | 265 | 128,137 | 1 | CA>CA |
| MT903344.1 | 133177 | 133178 | 43.932 | ATCTT | A | True | 265 | 128,137 | 1 | AT>AT |
| MT903344.1 | 133178 | 133179 | 1.712 | TC | T | True | 265 | 128,137 | 1 | TC>TC |
| MT903344.1 | 150480 | 150481 | 41.525 | C | T | False | 273 | 132,141 | 1 | CA>TA |
| MT903344.1 | 150560 | 150561 | 4.469 | AG | A | True | 273 | 132,141 | 1 | AG>AG |
| MT903344.1 | 150560 | 150561 | 35.706 | AGGATATGAT | A | True | 273 | 132,141 | 1 | AG>AG |
| MT903344.1 | 150566 | 150567 | 2.716 | TG | T | True | 273 | 132,141 | 1 | TG>TG |
| MT903344.1 | 151472 | 151473 | 25.362 | A | C | False | 228 | 117,111 | 1 | AG>CG |
| MT903344.1 | 155806 | 155807 | 27.605 | G | A | False | 243 | 125,118 | 1 | GG>AG |
| MT903344.1 | 162342 | 162343 | 40.414 | C | T | False | 343 | 180,163 | 1 | CT>TT |
| MT903344.1 | 170273 | 170274 | 52.291 | G | A | False | 229 | 107,122 | 1 | GG>AG |
| MT903344.1 | 170907 | 170908 | 8.712 | CT | C | True | 204 | 97,107 | 1 | CT>CT |
| MT903344.1 | 178220 | 178221 | 53.859 | G | A | False | 97 | 39,58 | 1 | GA>AA |
| MT903344.1 | 181063 | 181064 | 13.079 | TG | T | True | 250 | 125,125 | 1 | TG>TG |
| MT903344.1 | 181995 | 181996 | 36.192 | G | A | False | 287 | 142,145 | 1 | GA>AA |
| MT903344.1 | 183534 | 183535 | 42.234 | C | T | False | 226 | 114,112 | 1 | CC>TC |
| MT903344.1 | 186593 | 186594 | 36.025 | G | A | False | 283 | 149,134 | 1 | GA>AA |
| MT903344.1 | 193407 | 193408 | 37.356 | G | A | False | 192 | 107,85 | 1 | GA>AA |
| MT903344.1 | 193703 | 193704 | 44.138 | C | T | False | 158 | 90,68 | 1 | CG>TG |
| MT903344.1 | 194114 | 194115 | 51.278 | C | T | False | 164 | 94,70 | 1 | CC>TC |
| MT903344.1 | 194634 | 194635 | 49.215 | C | T | False | 138 | 80,58 | 1 | CC>TC |
| MT903344.1 | 195963 | 195964 | 59.943 | C | T | False | 85 | 51,34 | 1 | CA>TA |
| MT903344.1 | 196615 | 196616 | 18.346 | CAA | C | True | 34 | 21,13 | 1 | CA>CA |
Quick assembly of the reads. Below the contigs are displayed as mapped to the reference chosen for analysis.
The table below highlights versions of key software used within the analysis.
| Name | Version |
|---|---|
| pysam | 0.21.0 |
| fastcat | 0.14.1 |
| bedtools | v2.31.0 |
| flye | 2.9.2-b1786 |
| bcftools | 1.18 |
| medaka | 1.11.1 |
The table below highlights values of the main parameters used in this analysis.
| Key | Value |
|---|---|
| help | False |
| version | False |
| fastq | test_data/fastq/barcode01 |
| bam | None |
| out_dir | wf-mpx |
| sample | None |
| assembly | True |
| medaka_options | None |
| min_coverage | 20 |
| aws_image_prefix | None |
| aws_queue | None |
| disable_ping | False |
| monochrome_logs | False |
| validate_params | True |
| show_hidden_params | False |
| schema_ignore_params | show_hidden_params,validate_params,monochrome_logs,aws_queue,aws_image_prefix,wf |
| wf | {'example_cmd': ['--fastq wf-mpx-demo/fastq/barcode01'], 'agent': 'cw-ci', 'container_sha': 'sha22fc487196cad3768c9287fec8bf8524431d01a4', 'common_sha': 'sha91452ece4f647f62b32dac3a614635a6f0d7f8b5', 'medaka_sha': 'sha61a9438d745a78030738352e084445a2db3daa2a'} |
| _reference | /builds/zdQY-a-d/0/epi2melabs/workflows/wf-mpx/data/references/MT903344.1.fasta |
| _genbank | /builds/zdQY-a-d/0/epi2melabs/workflows/wf-mpx/data/references/MT903344.1.gb |
This report was produced using the
epi2me-labs/wf-mpx. The
workflow can be run using nextflow epi2me-labs/wf-mpx --help
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