Validation¶
bsaseq reproduces published results across two systems that differ in genome size,
trait type, and upstream pipeline.
Sorghum ms8 male sterility¶
Data: Xiao et al. 2025 (Genetics), NCBI BioProject PRJNA1134249 (SRR29793691-94). Default parameters.
| Region | Max Z | Variants |
|---|---|---|
| Chr04:61,000,001-63,000,000 | 12.3 | 35 |
| Chr04:56,750,001-58,750,000 | 6.11 | 131 |
| Chr09 | 5.69 | 18 |
| Chr01 | 4.46 | 102 |
The top region contains the causal variant at 61,494,009 (a bHLH transcription factor), matching the published mapping interval (Chr4:58.3-62 Mb). Secondary Chr09/Chr01 peaks are low and consistent with background. The published pipeline used Bowtie2 v2.2.9 + SAMtools v1.11 + bcftools + SnpEff v4.3a.
Rice root-knot nematode resistance¶
Data: Lahari et al. 2019 (Euphytica), an F2 population segregating for resistance.
| Region | Max Z | Variants |
|---|---|---|
| Chr11:28,250,001-29,500,000 | 3.46 | 21 |
| Chr09:20,250,001-21,500,000 | 3.08 | 1 |
The Chr11 region falls entirely within the published 23-29 Mb QTL but is ~5x narrower
(1.25 Mb vs ~6 Mb). Unlike QTL-seq, bsaseq did not require parental data. The published
pipeline used QTL-seq v1.4.4 + BWA-MEM v0.7.12 + FreeBayes v0.9.14.
Performance¶
Whole-genome runs on a SLURM cluster (Intel Xeon, 16 GB allocation):
| Dataset | Genome | VCF records | Passed | Windows | Runtime | Peak memory |
|---|---|---|---|---|---|---|
| Sorghum ms8 | ~730 Mb | 769,272 | 140,219 | 2,613 | 21.2 s | 0.28 GB |
| Rice nematode | ~390 Mb | 3,552,893 | 198,409 | 1,499 | 41.3 s | 0.25 GB |