Table 1.
Top: Comparison of BigWig-enabled tools when computing coverage sums over repetitive-element intervals for 10 GTEx brain tissue BigWigs and Bottom: Comparison of BAM-enabled tools when computing coverage means over exome intervals for a 30× WGS BAM
| Tool | Relative time | Run time | Memory (MiB) | BAM input | BigWig input | MacOS | Windows native | R interface |
|---|---|---|---|---|---|---|---|---|
| Megadepth (BigWig) | 1.00 | 1 m:57 s | 543 | Yes | Yes | Yes | Yes | Yes |
| megadepth-R (BigWig) | 2.13 | 4m:09 s | 808 | Yes | Yes | Yes | Yes | Yes |
| WiggleTools (BigWig) | 4.06 | 7 m:54 s | 10,379 | Yes | Yes | Yes | No | No |
| pyBigWig | 68.13 | 2 h:12 m:36 s | 7 | Yes | Yes | Yes | No | No |
| bwtool | 90.48 | 2 h:56 m:06 s | 750 | No | Yes | No | No | No |
| rtracklayer | 100.61 | 3 h:15 m:49 s | 14,074 | Yes | Yes | Yes | No | Yes |
| Megadepth (BAM) | 1.00 | 2 m:17 s | 1,016 | Yes | Yes | Yes | Yes | Yes |
| Mosdepth | 5.58 | 12 m:43 s | 1,911 | Yes | No | Yes | No | No |
| Samtools | 40.05 | 1 h:31 m:20 s | 15 | Yes | No | Yes | Yes | Yes |
| Sambamba | 3.55 | 8 m:05 s | 157 | Yes | No | Yes | No | No |
| WiggleTools (BAM) | 628.56 | 23 h:55 m:13 s | 372 | Yes | Yes | Yes | No | No |
Note: Each tool’s features are also summarized. All runs use a single thread except WiggleTools, which non-optionally uses extra threads for input and output.