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### Description of feature
Dear nf-core & pangenome team,
I have a few questions about your great program.
Based on the link (https://github.com/nf-core/pangenome/blob/1.0.0/modules/nf-core/w…
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I might have missed this, but is there a tool to stitch together two complementary hal alignments? I am facing resource limitations is running alignments with many species all at once, and I was think…
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what's wrong with my result using cactus-v2.8.1?!
**Input newick tree:** ((((((Glycine_max,(Fragaria_vesca,(Cucumis_sativus,Juglans_nigra))),Arabidopsis_thaliana),Vitis_vinifera),(Ambrosia_artemisi…
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After uploading the Fastq file and ref genome (.gnk), submit the Alignments mission. Then it shows ERROR, and I open the 'bwa_align.error' file and see the following error. I'm not sure what's going o…
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as of the merge of #160, charcoal now performs the following steps -
1. find candidate genomes for contamination analysis, based on sourmash shared hashes with GTDB r95
2. download genomes and per…
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Dear developer,
I encountered an error while plotting data with the tool. The error message is: "[pafToBins] Binning PAF alignments, binsize=10000bpError in GenomicRanges::tileGenome(seqlengths = aln…
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**Snakemake version**
Note the Snakemake **and** snakemake-wrappers version for which you experience the bug.
Always make sure to try out the latest version of both before creating a new bug rep…
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I'm using BREAKER2 to generate Augustus hints from RNA and Protein alignments. I'd prefer to use these hints as the protein-to-genome alignments found by GenomeThreader (BREAKER2) are usually better t…
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Dear Brian,
I am using EVM in a genome with some bona fide intronic genes, yet when I try this:
```
EVidenceModeler-1.1.0/EvmUtils/write_EVM_commands.pl \
--genome genome.fasta --weights `pwd…
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Hi there! I executed the steps listed in the readme to create a conda environment and install RibDif2 and its dependencies, then tried to run:
ribdif -g Ruegeria
But I get the following output,…