SamQL performance. A–C From left to right, the plots correspond to runtime for printing and counting SAM entries on increasing subsets of the input data for different queries. The used queries are: A string query on tag “CC:Z” (A); a numeric query on tag NH:i (B); A range query (C). The corresponding SamQL query is shown at the top. D Parallelization performance for BAM output for a range query (left) and the NH:i tag (right) on a large BAM dataset of approximately 900 million reads. For NH:i only 10% of the file was processed to keep the execution times reasonable. SamQL is inherently concurrent and cannot be limited to less than 2 threads which is why performance is equivalent at 1 and 2 threads. Colors correspond to SamQL using all threads (dark blue), SamQL bound to 2 cores (green), SAMtools (light green), naive Bash/Awk (cyan), BamTools (yellow) and Sambamba (red). The raw data for the plots can be found in Additional file 1: Table S1.