samtools stats

# Get data
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR209/009/SRR2099969/SRR2099969_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR209/009/SRR2099969/SRR2099969_2.fastq.gz
wget ftp://ftp.ensemblgenomes.org/pub/release-32/bacteria//fasta/bacteria_0_collection/mycobacterium_tuberculosis_h37rv/dna/Mycobacterium_tuberculosis_h37rv.ASM19595v2.dna.toplevel.fa.gz
gunzip Mycobacterium_tuberculosis_h37rv.ASM19595v2.dna.toplevel.fa.gz
mv Mycobacterium_tuberculosis_h37rv.ASM19595v2.dna.toplevel.fa H37Rv.fa

# Get software
wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2 && tar -xvf samtools-1.9.tar.bz2 && cd samtools-1.9/ && make && cd ..
wget https://github.com/BenLangmead/bowtie2/releases/download/v2.3.5/bowtie2-2.3.5-linux-x86_64.zip && unzip bowtie2-2.3.5-linux-x86_64.zip 
git clone https://github.com/lh3/bwa.git && cd bwa && make && cd ../

# Mapping
./bowtie2-2.3.5-linux-x86_64/bowtie2-build H37Rv.fa H37Rv.fa
./bwa/bwa index H37Rv.fa
./bwa/bwa mem -t 20  H37Rv.fa SRR2099969_1.fastq.gz SRR2099969_2.fastq.gz | ./samtools-1.9/samtools view -@ 20 -b - | ./samtools-1.9/samtools sort -@ 20 -o SRR2099969_bwa.bam - 
./samtools-1.9/samtools index SRR2099969_bwa.bam 
./bowtie2-2.3.5-linux-x86_64/bowtie2 -p 20 -x H37Rv.fa -1 SRR2099969_1.fastq.gz -2 SRR2099969_2.fastq.gz | ./samtools-1.9/samtools view -@ 20 -b - | ./samtools-1.9/samtools sort -@ 20 -o SRR2099969_bowtie.bam - 
./samtools-1.9/samtools index SRR2099969_bowtie.bam 

# Check coverage from bwa BAM
samtools stats SRR2099969_bwa.bam Chromosome:10-11    | grep ^COV
# Check coverage from bowtie BAM
samtools stats SRR2099969_bowtie.bam Chromosome:10-11    | grep ^COV