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I think this issue is related to something that has been mentioned previously here, but I'm not sure that it is resolved.
I am using GSalign to align and call variants from a series of assembled ge…
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Nice tool!!! I also have a similar idea for developing such a tool to genotype all genes witch cnv for large cohorts. The problem is you used HPRC etc. to construct a database, how can I construct a n…
yeeus updated
2 weeks ago
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My code is as follows：
cactus-pangenome ./js grch38_pan.seqfile --reference GRCh38 --outDir ./grch38_pan --outName grch38_pan --gbz --giraffe --vcf --chrom-vg --refContigs $(for i in `seq 22`; do pr…
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**1. What were you trying to do?**
Call variants with vg. I'm trying to align of paired-end illumina reads from different bird individuals to a vg graph generated with the Cactus Pangenome Pipe…
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Hello, I am using Roary to generate a pan-genome with 682 .gff files obtained from Prokka.
The Roary command I'm using is python3 roary_plot.py --label mytree.newick the tree made by these command is…
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Hi,
We have dozens of plant HiFi assemblies of inbreeding line, my previous test work on pggb for parameters tuning. I noticed the newest version of cactus including updates of pangenome pipeline.…
baozg updated
2 years ago
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Hi all,
I'm running the Pangenome Pipeline using the latest Cactus binary realease (cactus-bin-v1.3.0.tar.gz). The first two steps went well, while the last one, cactus-align, returned me an error …
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## Failed `sanitize_fasta_header` jobs with `sqlite3.OperationalError: disk I/O error` in Cactus Pangenome on WSL Ubuntu 20.04
### Issue Description
I'm encountering an issue with Cactus Pangenome…
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Dumping this here so it's recorded somewhere. This reads in a signature with multiple minhashes, output by gather using the flag `--save-matches`.
```
library(dplyr)
library(rjson)
sig_json
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Hi again,
I have a few more burning questions:
1. In the example of ordered-histgrowth from this link (https://github.com/marschall-lab/panacus/blob/main/examples/ordered_pangenome_growth_statis…