Table 6 Computing performance of major functions using 23 exome sequencing samples on a 16 CPU workstation
From: SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data
Script | Function | #CPU | Peak RAM (Gb) | Time | Notes |
|---|---|---|---|---|---|
exon_qc | quality control | 1 | 6 | 10-20 min | Per sample |
sam2wig | generate wig file | 1 | 2 | 20-50 min | Per sample |
sam2pileup | generate pileup file | 1 | 3-7 | 1-4 hours | Per sample |
snp | annotate and filter snp and indels | 1 | 4 | 2-8 min | Per sample |
rpkm | quantify coverage on gene model | 1 | 4 | 4-16 min | Per sample |
cnv | copy number variation | 1 | 4 | 5 min | Per sample |
genotyping | genotyping file across samples | 1 | 8 | 4 hour | Across 23 samples |
phenotyping | coverage (expression) across samples | 1 | 5 | 10 min | Across 23 samples |
eqtl -m cis | Cis- EQTL | 1 | 3 | 1 hour | 1000 genome data |
eqtl -m trans | Trans-EQTL | 16 * | 3 | 7 days | 1000 genome data |