A Supporting Information for “Mapping-Friendly Sequence Reductions: Going Beyond Homopolymer Compression”

A.1 “TandemTools” dataset generation

This dataset was obtained by taking a human X chromosome HOR sequence, concatenating it 500 times with added mutations in order to obtain an approximately 1 Mbp long sequence. Then 1200 reads were simulated from the sequence using nanosim³¹⁸ and assembled using a centromere-tailored pipeline⁷⁴³. A 10kbp deletion was then added to this assembly. The resulting sequence is the one we refer to as the “Centromeric sequence”.

A.2 MSR performance comparison

A.3 Analyzing read origin on whole human genome

Figure A.1: Origin of correctly (teal) and incorrectly (red) mapped raw reads.
Distribution of the origin of correctly and incorrectly mapped simulated reads (in teal and red respectively) on the different chromosomes of the whole human genome. The dark grey rectangle for each chromosome represents the centromere of that chromosome. The lighter gray rectangle on chromosomes 13, 14, 15, 21 and 22 correspond to satellites denoted as “stalk”, another repetitive region.

Figure A.2: Origin of correctly (teal) and incorrectly (red) mapped reads, transformed with HPC.
Distribution of the origin of correctly and incorrectly mapped simulated reads (in teal and red respectively) on the different chromosomes of the whole human genome. The dark grey rectangle for each chromosome represents the centromere of that chromosome. The lighter gray rectangle on chromosomes 13, 14, 15, 21 and 22 correspond to satellites denoted as “stalk”, another repetitive region.

Figure A.3: Origin of correctly (teal) and incorrectly (red) mapped reads, transformed with MSR_E.
Distribution of the origin of correctly and incorrectly mapped simulated reads (in teal and red respectively) on the different chromosomes of the whole human genome. The dark grey rectangle for each chromosome represents the centromere of that chromosome. The lighter gray rectangle on chromosomes 13, 14, 15, 21 and 22 correspond to satellites denoted as “stalk”, another repetitive region.

Figure A.4: Origin of correctly (teal) and incorrectly (red) mapped reads, transformed with MSR_P.
Distribution of the origin of correctly and incorrectly mapped simulated reads (in teal and red respectively) on the different chromosomes of the whole human genome. The dark grey rectangle for each chromosome represents the centromere of that chromosome. The lighter gray rectangle on chromosomes 13, 14, 15, 21 and 22 correspond to satellites denoted as “stalk”, another repetitive region.

Figure A.5: Origin of correctly (teal) and incorrectly (red) mapped reads, transformed with MSR_F.
Distribution of the origin of correctly and incorrectly mapped simulated reads (in teal and red respectively) on the different chromosomes of the whole human genome. The dark grey rectangle for each chromosome represents the centromere of that chromosome. The lighter gray rectangle on chromosomes 13, 14, 15, 21 and 22 correspond to satellites denoted as “stalk”, another repetitive region.

A.4 Performance of MSRs on the Drosophila genome

Figure A.6: Results of the paftools mapeval evaluation on reads simulated and mapped to whole Drosophila melanogaster and Escherichia coli genomes.
MSRs E, F and P are shown in different shades of blue to differentiate them from other MSRs. Reads were simulated with nanosim, and mapped with minimap2. The E. coli genome was obtained from Genbank ID U00096.2

A.5 Key resource table

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