EMM_pipeline | R Documentation |
emm typing pipeline from WGS assemblies December 21 2023, Walter Demczuk & Shelley Peterson
EMM_pipeline(Org_id, SampleNo, curr_work_dir)
Org_id |
Organism to query: GAS, PNEUMO or GONO |
SampleNo |
Sample number associated with contig.fasta file |
curr_work_dir |
Start up directory from pipeline project to locate system file structure |
GAS emm typing: Takes Organism, Sample Number and queries a contig.fasta file. For the most current emm types go to: https://ftp.cdc.gov/pub/infectious_diseases/biotech/tsemm/ download the alltrimmed.fta file rename to "emm_trimmed.fasta" and place in the allele_lkup_dna folder in WADE GAS/emm then be sure to index it using MakeBlastDB
A table frame containing the results of the query
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.