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Hi,
I am struggling to workout and estimate minimal resources to run cactus for 100 genomes mammal size.
I can use CPUs, GPUs but I need to estimate amount of resource for an amount of time (project…
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Hi,
I have executed pyseer and I would like to map my unitigs not to the list of my input files but back to just one fasta/gff file that represents my pangenome.
This file contains representat…
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Hello,
I'm trying panTools for the first time to build a pangenome graph from 4 polished assemblies of ~70mb in size. I tried following the instructions, and the program starts, but then just sits t…
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calc-hash-presence.py from [pangenome-hash-cor](https://github.com/ctb/2024-pangenome-hash-corr), does not yet allow me to compare protein sketches instead of nucleotide sketches.
I'd like to comp…
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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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Hi,
I'm running cactus-pangenome with diploid data as input: two files per individual (14 fasta files), named as described in the docs. For 6 of the 7 individuals the vcf output is diploid, but one i…
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Hello there,
I want to build a pangenome for a genus of grasses (_Hordeum_) I am working on in order to do some analysis. I have been playing with `pggb` for a while now but I think is time to requ…
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Hi Robert,
Some questions about the pangenome tool Roary.
I have run roary with:
`bactopia --wf pangenome --bactopia output_SAB_20240522 --include included.txt --use_roary True --cd 95 --cleanu…
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**1. What were you trying to do?**
I wanted to perform augmentation using gam file mapped through vg giraffe on my pangenome graph.
**2. What did you want to happen?**
Successfully augmented grap…
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Hello, when i ran the braker3, i meet a question as follows:
FASTA index file /public/home/pengyan/bioproject/23.Chil_pangenome/01.data/10.ann-2/SC/03.brake/braker/GeneMark-ETP/data/genome.softmask…