Workflow and code for: Longitudinal gut virome analysis identifies specific viral signatures that precede necrotizing enterocolitis onset in preterm infants (Kaelin et al., Nat Microbiol. 2022 May;7(5):653-662).
Virome analysis
-Workflow
-QC script
-Contig building and mapping script
-taxonomizr script
-Decontam, alpha and beta diversity script
-LEfSe script
-Prodigal and PHACTS script
-Maaslin2 script
Bacterial microbiome analysis (16S)
-Workflow
-QIIME2 script
-ANCOM-II parameters