Shotgun sequencing

Shotgun sequencing is a technology that breaks all microbial DNA into small pieces before sequencing.

The short pieces of sequenced DNA are called → short reads.

Short read tools

Analyzing short read samples from full genome shotgun sequencing

Short sequence reads are analyzed by → read mapping (alignment to reference sequences) or assembling into longer → contigs.

→ Alignment tools

Bowtie2, BWA,...

→ Assembly tools

SPAdes, MEGAHIT,...

→ Pathogen screening

screen for marker genes or strains in short-read samples