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- Two main data generation strategies: (1) amplicon sequencing and (2) shotgun sequencing
- At this time analysis one can choose calling variants or performing within-host evolution analyses inclu…
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Dear VG Team Members,
I hope this message finds you well.
While using the vg giraffe tool to align short reads, I encountered an issue similar to the one described in issue #4171 . Specifically,…
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Our group is developing software, PHG (Practical Haplotype Graph, https://github.com/maize-genetics/phg_v2), that makes use of TileDB-VCF to store VCF files. Our own code is written using Kotlin, a po…
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Hello,
I used the HPRC pangenome (https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/freeze1/minigraph/hprc-v1.0-minigraph-grch38.gfa.gz) to do the analysis. My processes to …
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The VCF spec contains this text on ALTs:
> Options are base Strings made up of the bases A,C,G,T,N,\*, (case insensitive)
or an angle-bracketed ID String (“\”) or a breakend replacement string as …
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Walk/W-lines are used to keep sequence walks through the graph. There are a few options:
1. Don't add W-lines as we already have Path/P-lines in GFA1. However, there are multiple problems with P-li…
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I'd like to query a part of the graph using coordinates against an arbitrary reference path encoded in it.
I have a implementation of this kind of feature that can serve as a conceptual starting poin…
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Hi,
I had apparently very good results -still yet to verify them- scaffolding about 5000 large Pacbio contigs vs a 750MB genome with results inside 1-2 days.
I would like to scaffold ~200,000 much…
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I produced nested PRGs (`--min_match_length`=7, `--max_nesting`=5) from multiple sequence alignments of plasmodium genes and found that `make_prg` can produce ambiguous PRGs.
Here's an example I…
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An issue has come up defining phasing of SVs. The SV phasing model needs to define an ordering of phased variants otherwise the haplotype would be ambiguous (e.g. a duplication has two SNPs, one on th…