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Top bioinformatics tools ranked by usage across 2063 tools.
| Rank | Tool | Usage | Trend | ||
|---|---|---|---|---|---|
| 359 | SNP-sites | Phylogenetics | Phylogenetics | 36.76 | +10% |
| 360 | Clair3 -- Long-Read Germline Variant Calling | Genomics | Genomics | 36.7 | +10% |
Data as of: Apr 12, 2026
| 361 |
| FlashLFQ |
| Proteomics |
| Proteomics |
| 36.7 |
| +10% |
| 374 | Singularity/Apptainer | Workflows | Workflows | 36.46 | +10% |
| 411 | fMRIPrep | Imaging | Imaging | 36.34 | +10% |
| 585 | Squidpy | Imaging | Imaging | 35.8 | +10% |
| 734 | Virsorter2 | Metagenomics | Metagenomics | 35.2 | +10% |
| 2 | SAMtools | Genomics | Genomics | 68.86 | +15% |
| 3 | DESeq2 | Transcriptomics | Transcriptomics | 68.08 | +15% |
| 4 | AlphaFold | Structure Prediction | Structure Prediction | 67.78 | +15% |