A single-page tool for building DNA and RNA-seq alignment commands.
Choose your experiment type, sequencing platform, and aligner — get a ready-to-run shell command with pros/cons analysis updated as you make selections.
Try it → kuod.github.io/alignment-picker
| Aligner | Data type |
|---|---|
| BWA-MEM2 | DNA short reads |
| BWA-MEM | DNA short + long reads |
| Bowtie2 | DNA short reads |
| Minimap2 | DNA long reads (PacBio, ONT) |
| STAR | RNA-seq short reads |
| HISAT2 | RNA-seq short reads |
| Salmon | RNA-seq quantification |
| Kallisto | RNA-seq quantification |
| Minimap2 | Long-read RNA-seq |
| vg giraffe | Pangenome / graph genome (short reads) |
| GraphAligner | Pangenome / graph genome (long reads) |
If you use this tool to build a pipeline, please cite the underlying aligner:
| Tool | Reference |
|---|---|
| BWA-MEM2 | Vasimuddin et al. IEEE IPDPS 2019. doi:10.1109/IPDPS.2019.00041 |
| BWA-MEM | Li H. arXiv:1303.3997 (2013). arxiv:1303.3997 |
| Bowtie2 | Langmead & Salzberg. Nature Methods 9, 357–359 (2012). doi:10.1038/nmeth.1923 |
| Minimap2 | Li H. Bioinformatics 34(18):3094–3100 (2018). doi:10.1093/bioinformatics/bty191 |
| STAR | Dobin et al. Bioinformatics 29(1):15–21 (2013). doi:10.1093/bioinformatics/bts635 |
| HISAT2 | Kim et al. Nature Biotechnology 37, 907–915 (2019). doi:10.1038/s41587-019-0201-4 |
| Salmon | Patro et al. Nature Methods 14, 417–419 (2017). doi:10.1038/nmeth.4197 |
| Kallisto | Bray et al. Nature Biotechnology 34, 525–527 (2016). doi:10.1038/nbt.3519 |
| samtools | Danecek et al. GigaScience 10(2):giab008 (2021). doi:10.1093/gigascience/giab008 |
| vg / vg giraffe | Sirén et al. Science 374(6574):abg8871 (2021). doi:10.1126/science.abg8871 |
| GraphAligner | Rautiainen & Marschall. Genome Biology 21:253 (2020). doi:10.1186/s13059-020-02157-2 |