Metagenomics Tools

→ 16S tools

QIIME, DADA2


→ Shotgun sequencing

Alignment, QC, remove host sequence, ...


→ Assembly

MEGAHIT, ...


→ BLAST

Blast format, E-value, FastANI, ...


→ Bowtie2

Reference database & mapping, ...


→ SAMtools

Coverage, consensus, SAM format, ...


→ Ubuntu / Linux server

gzip tar.gz sed awk, shell loop, ...