Table 1 Comparison of run time, memory, and storage space between Bazam and alternative processes for realignment. Timings encompass the end to end process starting from read extraction and ending with completion of realigned and sorted BAM files
From: Bazam: a rapid method for read extraction and realignment of high-throughput sequencing data
Tool | Storage used | Memory | Effective Cores | Time |
|---|---|---|---|---|
Sort-Extract-Realign | 282 GB | 20 GB | 16 | 13 h, 15 min |
Picard SamToFastq | 148 GB | 78 GB | 16 | 16 h, 14 min |
Biobambam bamtofastq | 149 GB | 30 GB | 16 | 15 h 30 min |
Bazam (no sharding) | 68 GB | 28 GB | 16 | 14 h, 55 min |
Bazam 10-way sharding | 102 GB | 20 GB | 160 | 1 h, 11 min |