Comments (2)
@ms-gx
I think vg will do this for you.
from minigraph.
@ms-gx
One can polish the graph from minigraph
using https://github.com/ComparativeGenomicsToolkit/cactus.
A real alternative could be https://github.com/pangenome/pggb. It can generate a pangenome graph from the all versus all alignments of the de novo genome assemblies which aims to mitigate reference bias.
from minigraph.
Related Issues (20)
- Masking regions for chaining?
- 0 reads mapped to graph HOT 3
- comparing --call output bed files with gfa file
- Valid paths in a GFA don't have end-to-end alignments HOT 1
- minigraph - stable fa - shot sequences
- Path/allele were could not be traced HOT 3
- Base-level alignments with -c -- comparison to MC HOT 2
- multiple mapping HOT 1
- description of `gfatools view -l` file HOT 2
- feature requests for output VCF HOT 1
- Illegal instruction HOT 2
- Graph construction methods HOT 2
- problem converting merged bed to vcf HOT 6
- size difference when reciprocal minigraphing
- Incorrect path alignment
- Empty alignment gaf output HOT 4
- some warnings while generating a genome graph
- Handling of read errors in input sequences HOT 1
- final link failed: Nonrepresentable section on output
- running minigraph HOT 1
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from minigraph.