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I have a sequence of `27bp length`, and I want to find out the `exact match of this sequence, and all the sequences that have 1 mismatch and 2 mismatch`, by the method of graph.
I used `bowtie1` to…
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The gene alignment step can take a long time to complete. Is it possible to add functionality to output the unaligned gene sequences to later align batches of them across a computing cluster? The pira…
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Do vg filter out some variants during the construction of the pan-genome, and if so, what are the criteria for filtering? The number of variations in the pan-genome is reduced compared to the variatio…
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Hi. I'm trying to run 84 genomes through micropan. I'm getting an error that must be related to the number of genomes, but wanted to run it past you. Any ideas for a fix other than reducing the genome…
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Hello author, I have a question about reference-free methods. Progressive Cactus is a reference-free multi-genome alignment, and it seems to be independent of the reference genome during the alignment…
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Hello,
May I sort the dot plot graph by the name of chromosomes from the genome reference?
thank you!
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I was wondering if interchromosomal translocations can be included in the graph genome generated by cactus. Thank you for your response!
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#### Summary:
We need a way to generate benchmark test data to ensure consistency and accuracy of `pyani` output.
#### Description:
The initial plan is to take a single genome sequence as input (…
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I think it would be helpful to include in the sourmash documentation on how to interpret the charts and graphs that sourmash produces.
I may suggest
- adding information in a [side text](https://…
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**1. What were you trying to do?**
Use vg giraffe to map wgs reads to a graph.
**2. What did you want to happen?**
The program to run to completion without issue, or at least provide some debuggi…