Difference between revisions of "Mitohifi"
| Line 58: | Line 58: | ||
If you publish research that uses {{#var:app}} you have to cite it as follows: | If you publish research that uses {{#var:app}} you have to cite it as follows: | ||
| − | When using MitoHifi, please cite | + | When using MitoHifi, please cite their Zenodo: |
DOI: 10.5281/zenodo.5205678 https://zenodo.org/record/5205678#.YlVMIi8w1TY | DOI: 10.5281/zenodo.5205678 https://zenodo.org/record/5205678#.YlVMIi8w1TY | ||
| − | |||
| − | + | And please cite MitoFinder: | |
Allio, R, Schomaker‐Bastos, A, Romiguier, J, Prosdocimi, F, Nabholz, B, Delsuc, F. MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics. Mol Ecol Resour. 2020; 00: 1– 14. https://doi.org/10.1111/1755-0998.13160 | Allio, R, Schomaker‐Bastos, A, Romiguier, J, Prosdocimi, F, Nabholz, B, Delsuc, F. MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics. Mol Ecol Resour. 2020; 00: 1– 14. https://doi.org/10.1111/1755-0998.13160 | ||
| − | + | For tRNAs annotation: | |
Laslett, D., & Canbäck, B. (2008). ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics, 24(2), 172-175. | Laslett, D., & Canbäck, B. (2008). ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics, 24(2), 172-175. | ||
Latest revision as of 17:01, 21 July 2022
Description
MitoHiFi is a python workflow that assembles mitogenomes from Pacbio HiFi reads.
Environment Modules
Run module spider mitohifi to find out what environment modules are available for this application.
System Variables
- HPC_SINGULARITY_IMAGE - singularity image
Citation
If you publish research that uses mitohifi you have to cite it as follows:
When using MitoHifi, please cite their Zenodo:
DOI: 10.5281/zenodo.5205678 https://zenodo.org/record/5205678#.YlVMIi8w1TY
And please cite MitoFinder:
Allio, R, Schomaker‐Bastos, A, Romiguier, J, Prosdocimi, F, Nabholz, B, Delsuc, F. MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics. Mol Ecol Resour. 2020; 00: 1– 14. https://doi.org/10.1111/1755-0998.13160
For tRNAs annotation:
Laslett, D., & Canbäck, B. (2008). ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics, 24(2), 172-175.