Supplementary Data for "Mapper: fast and accurate sequence alignment via gapped x-mers"

Evaluation Results:Suboptimal alignment rates:The folder "alignment_accuracy/" and "alignment_accuracy_ANI" contains the following:Alignment results for the same read compared across different aligners. Files ending with withtag.txt represent all alignment results, while files ending with withtagclean.txt exclude middle soft clips reported by BWA and Minimap2.A summary of suboptimal alignment rates.Potential causes of suboptimal alignments.Code to visualize the results (Figures 4, 5, S1, and S3) is available at https://github.com/caozhichongchong/Mapper_eva (Alignment_accuracy.ipynb and Alignment_accuracy_ANI.ipynb)Alignment inconsistency rate:The folder "alignment_consistency/" contains a summary of alignment inconsistency rates and suboptimal alignment rates.Code to visualize the results (Figures 6 and S4) is available at https://github.com/caozhichongchong/Mapper_eva (Alignment_consistency.ipynb)Speed:The folder "speed_evaluation" contains runtime and memory usage data for all aligners during library indexing and read alignment.Code to visualize the results (Figures 7, S5. and S6) can be found at https://github.com/caozhichongchong/Mapper_eva (Alignment_accuracy.ipynb)Alignment example for Figure S2: The folder "alignment_example" contains the code and SAM files supporting the alignment results for an example read shown in Figure S2.