RNA-seq and Tn-seq reveal fitness determinants of vancomycin-resistant Enterococcus faecium during growth in human serum, from paper by Xinglin Zhang et al.
Basic analyses:
- Genome assembly with PacBio reads.
- Assembly evaluation.
- Structural and functional annotation.
- Synteny comparison with a closely related genome.
- Reads preprocessing: trimming + quality check (before and after)
- RNA-Seq reads alignment against the assembled genome.
- Differential expression analysis between rich medium and heat-inactivated serum conditions.
Extra analyses:
- Genome assembly with Illumina and Nanopore reads (SPAdes).
- Assembly evaluation (extra method: MUMmerplot).
- Plasmid identification.
- SNPs calling.
- Evaluate antibiotic resistance potential.
- Identify essential genes for growth in human serum based on the Tn-Seq data analysis.