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Hi,
I assembly a plasmid sequence data with raven but get no `fasta` output, but there are `three seq records` in `gfa file`(I run flye and canu with same sequence file and all output an assembled …
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Back at MemPan23, we heard the following refrain a few times:
> Pangenomics is one of those fields that have been "solved" by the discovery of the right data structure. That data structure is the GFA…
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Hello, I am running `vg autoindex` to splice the minigraph-cactus full pangenome according to GENCODE v44 gene annotations in order to map RNA-seq reads. I have two questions:
1) By running the follo…
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can somebody help me with this error:
filter_stdout, filter_stderr = cactus_call(parameters=filter_paf_cmd, check_output=True, returnStdErr=True, job_memory=job.memory)
File…
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Hi, I've tried to convert a GFA 3 tokenized source to a .LST file, but I've received the error:
> Version 3 files not supported yet.
By looking at the source code, in fact, it seems that the sou…
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Hello,
Thank you very much for abPOA, it is a nice tool, installation was fast and easy.
I would like to be able to incrementally update the POA graph. That would be very practical to use the …
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**1. What were you trying to do?**
I was trying to extract a subregion from a graph encoded in a GFA format file.
**2. What did you want to happen?**
I want to obtain a GFA format file with the g…
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What are the best ways to encode a translocation and an inversion in `.gfa` file format? Could you please provide an example for each variant? Thank you!
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Adding ability to output `layout` results in `GFA` format would allow us to use bandage tool for drawing assembly from command line.
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Hello,
I have successfully ran both the Cactus pipeline on a set of ~30 bacterial genomes, as well as on the mammals example data.
Both times Cactus has output a .hal file that I can inspect and v…