320    ◾    Bioinformatics

do

samtools faidx ${i}

done

bowtie2-build healthy_scaffolds.fasta healthy

bowtie2-build moderate_scaffolds.fasta moderate

bowtie2-build severe_scaffolds.fasta severe

Once the index has been built, we can use Bowtie2 to align the FASTQ reads to their

respective “scaffolds.fasta”.

mkdir sam_assemblies

bowtie2 --sensitive-local \

-p 4 \

-x assemblies/healthy \

-1 fastq_pure/ERR1823587_pure_R1-50.fastq.gz \

-2 fastq_pure/ERR1823587_pure_R2-50.fastq.gz \

-S sam_assemblies/ERR1823587_healthy.sam

bowtie2 --sensitive-local \

-p 4 \

-x assemblies/moderate \

-1 fastq_pure/ERR1823601_pure_R1-50.fastq.gz \

-2 fastq_pure/ERR1823601_pure_R2-50.fastq.gz \

-S sam_assemblies/ERR1823601_moderate.sam

bowtie2 --sensitive-local \

-p 4 \

-x assemblies/severe \

-1 fastq_pure/ERR1823608_pure_R1-50.fastq.gz \

-2 fastq_pure/ERR1823608_pure_R2-50.fastq.gz \

-S sam_assemblies/ERR1823608_severe.sam

We can notice that there are some statistics when the alignment process finishes for each

sample.

We will convert SAM files to bam files and then we will sort the alignments in the BAM

files.

cd sam_assemblies

samtools view -S -b ERR1823587_healthy.sam > ERR1823587_healthy.

bam

samtools view -S -b ERR1823601_moderate.sam > ERR1823601_moderate.

bam

samtools view -S -b ERR1823608_severe.sam > ERR1823608_severe.bam

for i in $(ls *.bam);

do

samtools sort -@ 4 ${i} -o ${i}.sorted

done