bowtie2-build toy_dataset_contig_for_mapping.fasta toy_dataset_contig_for_mapping.btindex
bowtie2 -x toy_dataset_contig_for_mapping.btindex -f -U toy_dataset_reads_for_mapping.fasta -S toy_dataset_mapped_species1.sam
samtools sort toy_dataset_mapped_species1.bam -o toy_dataset_mapped_species1_sorted.bam
samtools index toy_dataset_mapped_species1_sorted.bam
