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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,...

    SPAdes, MEGAHIT,...
    screen for marker genes or strains in short-read samples