Metagenomics Tools

Sequence data analysis

→ 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, ...