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Hello,Professor
I have two assembly genome of two species. I want to construct a graph from the two genome using PGGB. I firstly combine the two genome into a input.fa ,then index the input.fa , fina…
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**1. What were you trying to do?**
calling structural variation after mapping long-read data on whole genome pangenome graph
**2. What did you want to happen?**
create a VCF file which contai…
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Hi,
I have built the Graph Pan-genome, how should I use the tool to characterize it and dig deeper into the potential information it contains. Or is there any other analysis tool recommended.
Best…
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Hello,
I'm also keen to integrate into the genome graph the structural variability detected by Sv callers (from short reads and/or long-reads). I was wondering if minigraph handles that?
Those are …
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Dear Linxing,
Good afternoon. Thank you for this excellent paper and tool! I read this paper and shared it with my lab members. I have some questions about the application of COBRA:
1. For the…
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Hi there
This is another clarification question:
(1)
Is there a recommended way to count the number of mapped reads against a graph? Currently, I've been parsing the JSONs (which were create…
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I'm attempting an assembly (relatively heterozygous diploid genome; 5Gb haploid size; with Hifi, ONT & Hi-C).
In the directory 7-consensus, the uniting-popped fast = 7.3Gb; however the uniting.popp…
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This came up in the code review yesterday (@tanaes). It would be great to relate the sequences into a coherent entity in order to represent contigs in one genome or pan-genomes. We argue that it shoul…
RNAer updated
5 years ago
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Hey, I am trying to run example code in your repo(sequences.txt) with some modifications in local system but I am having this problem.
```
$ python3 ./gengraphTool.py make_genome_graph --seq_file …
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Howdy,
My name is Per and I would first like to thank you for developing Flye!
Anyway, I have been using Flye to assemble an *E. Coli* isolate from ONT data.
I think that Flye is having 2…