Shotgun Metagenomic Data Analysis    ◾    319

mkdir assemblies

cp metag_healthy/scaffolds.fasta assemblies/healthy_scaffolds.

fasta

cp metag_moderate/scaffolds.fasta assemblies/moderate_scaffolds.

fasta

cp metag_severe/scaffolds.fasta assemblies/severe_scaffolds.fasta

Then, we can use Samtools and Bowtie2 to build an index for each “scaffolds.fasta” file of

each sample.

cd assemblies

cd assemblies

for i in $(ls *.fasta);

FIGURE 8.5  The metagenomic composition of the healthy individual.