Using hisat2-build, we created separate indices for the human genome and the mouse genome using toplevel fasta DNA sequence files from the Ensembl ftp site (GRCh38 [hg38] or GRCm38 [mm10], respectively). After building the indices, we used HISAT2 to align each of the 5 pairs of mixed fastq files with a range of species compositions using each index. The result was 5 SAM files for human and 5 for mouse. The number of non-matching and matching reads in each SAM file was recorded.
