Code from microbime analysis for manuscript:
Sub-clinical intestinal inflammation prior to Salmonella infection predisposes mice to become super-shedders,
by Audrey Chong, Zee Kwong, Mina P. Peyton, Laszlo Kari, Angelina G. Angelova, Diane Cockrell, Jared McGourty, and Olivia Steele-Mortimer
Seq data submitted to SRA:
BioProject: PRJNA1297215
SRA numbers: SAMN50214516 - SAMN50214808 \
raw reads were de-weaved, then QC-ed with fastp and mutiQC
input data for analysis was the Trimmed, Error-Corrected and Decontaminated (TED) reads produced by Nephele.
Taxonomic annotations were produced with Kraken2 as part of Nephele, against the mouse gut database MGBCdb.
Subsequently, the unclassified reads were further classified with RefSEQdb (krPLUS) for the Salmonella fraction.
'Salmonela_sp" taxonomies were treated as 'Salmonela enterica'.