Analyzing → short-read samples from full genome shotgun sequencing
Short-read sequencing data are analyzed by → read mapping (alignment to reference sequences) or → assembling into longer → contigs.
→ Alignment tools (read mapping)
Bowtie2, BWA,...
SPAdes, MEGAHIT,...
screen for marker genes or strains in short-read samples
download public available shotgun sequencing samples
read quality trimming and adapter removal
remove reads associated to the human host