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I'm very interested in the new --core and --assign options added to orthofinder3.
I launched orthofinder3 on 1000 genomes with the following command:
` orthofinder -t 40 -M 'msa' -f input/core/ …
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Hi,
I would be interested into a function that would enable to snapshot a channel without testing the md5sum of the files in it.
The rational behind that is that in nf-core we often want to know what…
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Dear author, thank you for your software. Plotsr can be used to plot syntenic regions, inversions, translocations regions and duplications regions. But, I couldn't plot large deletions regions betwee…
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Hi, I have two huge genomes (ref: 48G; query: 20G).
To obtain an accurate genome alignment, I tried to annotate the transposable element (TE) and filter the non-TE sequence longer than 50bp to be the…
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@jeizenga
hello, I read about issues with mapping long reads for pan-genomes, so I was wondering if the new version of vg giraffe supports mapping long reads.
[https://github.com/vgteam/vg/…
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i have added the specific genome of bacillus haynessi to get hit against it but even after confirmation of genomes has been added while running fastq screen, the specific genome is not used as refernc…
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Can you please link the fasta and gtf files that are used when "hg19" is entered as the 'reference' input?
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I would like to use the pipeline on a large plant genome. Would it be to run separately on chromosomes or directly on the entire genome? Are there any requirements for CPUs and RAM? Have you ever test…
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Hello, thanks for your development of this useful tools!
I met several issues when use EDTA2:
1) the file `$genome.EDTA.TEanno.split.density` didin't show the running result but the following conten…
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Hi, the software seems very good, but I am new in metagenome analysis and I have questions about the selection of appropriate reference genomes (indexes) when using 'hostile'.
1.
I read the "Refe…