FAQs
What information does the Core require to run?
The Core requires raw, paired-end Illumina sequencing data, and it requires a sample sheet.
What documents are made by the Core?
The name of an isolate is shown by '*'.
The addition of the isolate's Genus and species is shown by '#'.
| Folder names | Outputs |
|---|---|
| / | run_parameters.txt |
| / | software_version_report.txt |
| / | failure_summary.csv |
| 00_rawData/ | *_R1.fastq.gz |
| *_R2.fastq.gz | |
| 01_rawPrep/ | *_R1_001_val_1.fq.gz |
| *_R2_001_val_1.fq.gz | |
| 02_assemblies/ | fa/#*.fa |
| gfa/#*.gfa | |
| 03_QC/ | quast_report.tsv |
| seqTK.summary.csv | |
| NB501042_139_HFHHCAFXY_multiqc_report_data/ | |
| NB501042_139_HFHHCAFXY_multiqc_report.html | |
| counts/*_count.txt | |
| kraken2_raw/*_kraken2_reads.report | |
| 04_mass_screening/ | summary_'database'-75.tab |
| isolate/#*_'database'-75.tab | |
| 05_annotation/ | #*_.faa |
| #*_.fna | |
| #*_.gbk | |
| #*_.gff | |
| 06_taxonomy/ | summary_taxonomyTable.csv |
| isolate/*_ani.tab | |
| 07_phylogeny/ | sequencerID_run#_flowCellID.nwk |
What are the different folders?
The Core's file system contains the following files and folders:
| Directory names | Description of contents |
|---|---|
core.nf |
The Core nextflowscript. |
nextflow.config |
The nextflow config file. |
| input_core/ | Deposit the raw reads and sample sheet here. |
| output_core/ | Core deposits data here. |
| work/ | The Nextflow working directory. |
| config/ | Ignore. |
| downloads/ | Save your compressed data here. |
How do you view the output files?
You can open the files in a spreadsheet, e.g. MS Excel. The output files are in .tab format.
The run_parameters.txt document can be opened in any text editor.
Is there a limit to how many genome assemblies the Core can screen?
There is no lower or upper limit on how many genomes the Core can analyse.