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Hi, How to add new sample genomes and contigs to an existing pan-genome producted by PGGB, and whether it can be done directly using the Minigraph or GraphAligner tool. Any suggestions on how to do th…
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Dear devs,
I'm interested in visualizing a pangenome matrix from odgi pavs in JBrowse1.
Maybe someone has made something like this viewer, panache as an example.
https://www.appliedbioinforma…
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I'm trying to run cactus-pangenome to construct a pangenome of 6 different samples of the same species (including a reference). My invocation is below:
`cactus-pangenome ./js seqFile.txt --outDir ./o…
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## Motivation
Pangenomes are key to understanding the distribution of gene content and synteny across closely related genomes. Currently, the driving force behind this strategy is sequence alignmen…
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This is a request for a new feature rule to use PPanGGOLiN to create pagenome graphs for the genome projects.
I think we should use the Roary-defined Gene Famillies as input to `ppanggolin`. This w…
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I wrote a script that calculates the distribution of hashes in collections of genomes. one goal is to generate some statistics for what the pangenome overlap is between genomes. It's a pretty straight…
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+ [Application of a Novel “Pan-Genome”-Based Strategy for Assigning RNAseq Transcript Reads to Staphylococcus aureus Strains](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0145861)…
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Hi,
I'm running minigraph-cactus v2.8.1 for a small region of a genome with the following command:
```
singularity exec --contain --bind $(pwd):/data $SCRIPTS cactus-pangenome \
/data/jobstore $fa…
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Our use of objects instead of strings for graph creation slowed down performance, probably due to the additional allocation.
```
2019-06-19 14:33:34 panther prairiedog[21158] DEBUG Done graphing S…
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can somebody help me with this error:
filter_stdout, filter_stderr = cactus_call(parameters=filter_paf_cmd, check_output=True, returnStdErr=True, job_memory=job.memory)
File…