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Hi,
I would like to know how to parameterize Abyss to use a reference genome. I am having some trouble with MaSurca, so I wanted to try Abyss to see if the Busco Score is higher. I would like to sa…
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I did about 20 MaSuRCA assemblies recently using as insert size of 150 (PE= pe 150 22). I assume that this was wrong because the average PE read size was ~150. Regardless, the assemblies came out pret…
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Essentially, from what I can see... redundans has stalled completely once it reaches the stage of scaffolding. The files produced up to that point:
lrwxrwxrwx 1 lcampbell ensembl 243 Feb 21…
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Hello there,
Thanks for developing this program. I want to use it to annotate a fungal genome. However, when I tried to test the program with the example you provided for Saccharomyces cerevisiae, …
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I was wondering if I can avoid the correction step of my assembly and jumping directly to the trimming step and so on. My reads have been called with the SUP models in Guppy5+, but not sure if the Km…
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I have gene models for a MaSuRCA assembly, but it's not a great assembly. I used the online tool CoGe to create a "pseudo assembly, where it maps the MaSuRCA contigs onto a higher quality reference fo…
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Hello,
I'm trying to use Canu on the grid and I'm a bit confused of setting options to get the result for max possible shortest time.
command in terminal:
`/home/vshapovalova/canu-2.2/bin/canu -p…
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@yuantianhpc when you have time, we'll need a list of tools here that can be containerized. Can use the task list (check box) in the above so anyone working on this can help generate them or point to…
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I want to assembly a genome from paired-end Illumina short reads (2x150). I realize this will be fairly fragmented, for my purposes that is ok for now. I just need to estimate the system resources to …
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The main issue appears to be that the masurca executable isn't linked in the end. I get this error from running install.sh -
```
./install.sh: 23: ./install.sh: /root/MaSuRCA-4.0.3/bin/masurca: …