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**1. What were you trying to do?**
I was attempting to make phased VCFs from pggb graphs made for the HPRC.
Let's take chr22 as a test case: https://s3-us-west-2.amazonaws.com/human-pangenomics/…
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As i try use PEPPER VERSION: 0.5.2 , at end of pepper_variant step , error like Could not read from vcf file:PEPPER_OUTPUT_SNP.vcf.gz
following case-study and i can generate the final table.
i use …
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Hello @labgem and @merenlab (@meren),
I've been using both PPAnGGOLiN and Anvio pangenomic pipelines and really loving both tools. I've used both tools independently with Prokka annotated .gff file…
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I have installed anvi'o in my miniconda3 (Ubuntu 18.04 LTS) laptop computer. I had successfully executed `anvi-self-test` and obtained proper output. I intended to do pan-genome (Included whole and dr…
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Adding more than 4 studies to a Windows Server 2019 virtual machine produces an error
When adding 5+ studies I get the following
"1 validation error detected: Value at 'provisingParameters.7.mem…
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Hi,
Recently I finished pangenomics analysis on my 124 MAGs. When I start the interactive mode the process gets killed at initialize gene clusters (on my 8 core i7-16GBram PC). If I use **--skip-in…
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## Short description of the problem
I have followed the tutorial at https://merenlab.org/2016/11/08/pangenomics-v2/
Using anvi-pan-genome I have created PAN-GENOME.db of 143 complete genomes.
Now…
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1. What is the topic of your lesson or lesson proposal?
Analysis of metagenomics and pangenomics data
I have enjoyed the Software Carpentry's Genomic lesson, and I think we can go further and deve…
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A "properly paired" read pair is a pair that aligns with the expected relative mate orientation and with the expected range of distances between mates. Is there a way to figure out which read pairs ar…
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Hi,
I've paired down my test data set to fail fast.
Here's the first error I could troubleshoot by changing naming convention
## Description of the bug
Input file names:
```bash
788K -rw-rw-r…