JSON
file (extension .json
), or multiple files, with their own plasmid data. These files are generated by pATLASflow, a pipeline to run mapping, mash screen and assembly methods for pATLAS. They can also be generated through FlowCraft recipesjson
files can be imported using a the Upload file...
button or by dragging and droping the files to the text box on the right of this button.nextflow run tiagofilipe12/pATLASflow --mapping --reads "your_folder/*.fastq"
JSON
file can then be provided to pATLAS in the Mapping menu.nextflow run tiagofilipe12/pATLASflow --mash_screen --reads "your_folder/*.fastq"
JSON
file can then be provided to pATLAS in the Mash screen menu.nextflow run tiagofilipe12/pATLASflow --assembly --fasta "your_folder/*.fasta"
JSON
file can then be provided to pATLAS in the Assembly menu.JSON
input users must run the following command:nextflow run tiagofilipe12/pATLASflow --mapping --mash_screen --reads "your_folder/*.fastq"
JSON
file can then be provided to pATLAS in the Consensus menu.results
. These files can be uploaded to their respective menus within the pATLAS sidebar menu.flowcraft.py report
module to generate interactive reports that can send requests to pATLAS directly without importing a file to pATLAS.> 0
it means that the plasmid1 is the "best hit". If this result is < 0
it means that the plasmid2 is a "better hit" than plasmid1. However, if calc results is = 0
this means that both are "best hits".percentage
is the percentage of the queried plasmid that is covered by HTS data, resulting from mapping.identity
is the percentage identity, from the mash screen output, of the queried plasmid and the HTS data.> 0
it means that the plasmid1 is the "best hit". If this result is < 0
it means that the plasmid2 is a "better hit" than plasmid1. However, if calc results is = 0
this means that both are "best hits".identity
is the percentage identity, from the mash dist output, of the queried plasmid and the HTS data Note 2: shared hashes
is a measure of the percentage of sequence that are shared between the HTS data and the plasmid. This is useful because mash dist reports identity of the smallest sequence against the larger sequence.> 0
it means that the plasmid1 is the "best hit". If this result is < 0
it means that the plasmid2 is a "better hit" than plasmid1. However, if calc results is = 0
this means that both are "best hits".