Read the instructions for how to register
We are accepting:
.bam Reads aligned to the MN908947.3 \ NC_045512 reference. The BAM must be sorted and unmapped reads must be filtered. If you used the ARTIC pipeline, provide the untrimmed BAM..fa|.fas|.fasta Consensus sequence as FASTAArrange your DATA_DIR by creating a directory for each sequencing run.
Each run directory should be named with your sequencing run_name, exactly as it appears in the associated metadata.
Inside each run directory, you should create a directory for each sample, named with the sample’s central_sample_id, exactly as it appears in your metadata.
You must name your directories in this way to ensure they are collected by the system when your metadata is uploaded.
The file names are less important, but must end with the right file extension to be detected (see list above). In lieu of a formal unified naming scheme at this time, please ensure that your sample directories are named such that you will be able to identify them in the future and at the least, are unique to your site.
As an example, the following data_dir contains two runs with two samples each:
| data_dir/
|--| 200320_M00001_0001
|--| BIRM-XXXXX
|-- alignment.bam
|-- consensus.fa
|--| BIRM-YYYYY
|-- alignment.bam
|-- consensus.fa
|--| 200320_M00001_0002
|--| BIRM-AAAAA
|-- alignment.bam
|-- consensus.fa
|--| BIRM-BBBBB
|-- alignment.bam
|-- consensus.fa
Further runs on the same sample can be added in future by adding a new run directory and re-using the original sample name. Do not delete the old data.
| data_dir/
|--| 200320_M00001_0001
|--| BIRM-XXXXX
|-- alignment.bam
|-- consensus.fa
|--| BIRM-YYYYY
|-- alignment.bam
|-- consensus.fa
|--| 200320_M00001_0002
|--| BIRM-AAAAA
|-- alignment.bam
|-- consensus.fa
|--| BIRM-BBBBB
|-- alignment.bam
|-- consensus.fa
|--| 200320_M00001_0003
|--| BIRM-AAAAA
|-- alignment.bam
|-- consensus.fa
|--| BIRM-BBBBB
|-- alignment.bam
|-- consensus.fa
rsync -av --progress **DATA_DIR** **USERNAME**@bham.covid19.climb.ac.uk:upload/
scp -r **DATA_DIR** **USERNAME**@bham.covid19.climb.ac.uk:upload/
Recall your username begins with climb-covid19-.
See providing metadata.
You will not be able to run analyses of your samples on climb without providing metadata.
You may check your upload was successful by logging in with SSH:
ssh **USERNAME**@bham.covid19.climb.ac.uk