Wenhai Zhang

How to get all information of reads mapped to all paths instead of a reference path?

11

Hi, I want to map short reads to a large gfa graph and get the reads information about which paths mapped to and which postion (nodes id) in the paths....

`vg giraffe` Split alignments cannot be converted to named-segment-space GAF

7

**1. What were you trying to do?** map reads to the graph with `vg giraffe`. **2. What did you want to happen?** get the GAF with original GFA node IDs....

camisim encountered an error when specifying the --hmm_model parameter in pbsim2

3

Hi, I modified script "readsimulationwrapper.py" to use pbsim2 to simulate pacbio CLR reads.  When I set "--sample-fastq" parameter to simulate pacbio HiFi reads, it work well. But when I...

Genomes used to build the database

1

Could you provide me with the assembly_accession of the Escherichia coli (1433) used to build the database? Thank you in advance!

huggingface_hub dowload failed

1

### Describe the bug I checked the source of error "Distant resource does not have a Content-Length." The error seems to be caused by the size being None in the...

Chromosome path not found in graph or haplotypes index

9

**1. What were you trying to do?** I used `vg rna` to build a spliced pangenome and a pantranscriptome with a GFA file from PGGB and a gff3 file. Similarly,...

Is it possible to get the path of genome in GFA format file?

2

Hi, I test `ggcat` with two similar genomes. From new version, I can get the GFA format file. But it only contains node information. I would like to know if...