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Update README.md
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baoxingsong authored Mar 5, 2024
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Expand Up @@ -79,7 +79,7 @@ In general, totally four commands are need to run through the whole pipeline.
* [AnchorWave use prior informations about whole genome duplication, chromosome rearrangement etc to guide the genome alignment, while AnchorWave could not figure out those evolution events automatically. Users need to know those informations before running AnchorWave and tune the parameters accordingly. Users might need to draw some plots to figure out if you would like to use `genoAli` or `proali`. If `genoAli` is proper, then need to think about if you would like to set `IV`.
If `proali` is proper, then need to think about how to set the values of `R`, `Q` and maybe `-e`.](#Note)
Could refer [guideline.pdf](./doc/guideline.pdf) or [#16](./issues/16) for how to do that.
* To alignment highly diverse genomes, the command 4 might cost a couple of CPU days. </span> If you have large memory available, this step could be paralyzed. Without heavily parameters turning, for highly diverse genomes, using a single thread, AnchorWave uses ~25Gb memory. Increasing a thread would cost an extra ~10Gb memory. If the two genomes have very similar sequences, the time and memory cost would be significantly less.
* To alignment highly diverse genomes, the command 4 might cost a couple of CPU days. </span> If you have large memory available, this step could be paralyzed. Without heavily parameters turning, for highly diverse genomes, using a single thread, AnchorWave uses ~20Gb memory. Increasing a thread would cost an extra ~10Gb memory. If the two genomes have very similar sequences, the time and memory cost would be significantly less.


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