apredeus/D37_salmonella_paper

all the code and small data files relevant to D37712 genome + RNA-seq paper

All scripts and data files relevant to D37712 paper

Publication

• Preprint: Salmonella enterica serovar Typhimurium ST313 sublineage 2.2 has emerged in Malawi with a characteristic gene expression signature and a fitness advantage
• Paper: under review

Raw data and assemblies

• RNA-Seq: GSE161403
• Genome assembly: ASM1425033v1
  • Illumina raw reads: SRR12444880
  • PacBio raw reads: SRR12444881

Content

• Genome assembly and annotation used for the processing
• Brief bioinformatics protocols
• Scripts used in genome and transcriptome analysis