Shotgun Sequencing Tools

Metagenomics Tools

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,...


→ Assembly tools

SPAdes, MEGAHIT,...


→ Pathogen screening

screen for marker genes or strains in short-read samples


NCBI SRA download

download public available shotgun sequencing samples


Read quality control

read quality trimming and adapter removal