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Recent Replies
Comment: magpurify errors
by
shevch2009
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I have checked with my eyes, and I didn't find it, I have only one contig that starts with k127_458 .... but the name is different - k127_4…
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So, you aren't sure about the exact species? Then you might want to be careful with reference-based assembly in general. I recommend the fo…
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Panos
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That's a very comprehensive list! Thanks for sharing!
`minigraph` better suits my needs because all I need is SVs for my genomes. As far a…
Comment: Yeast reference-based genome assembly
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amy967107
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I have ~2.01 Gb of ONT data and the target genome is ~20–23 Mb (90–100× coverage). My ONT read N50 is ~3.8 kb, so contiguity may be limited…
Comment: Yeast reference-based genome assembly
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amy967107
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This is a yeast strain (probably Rhodotorula spp.) and I'm trying to assemble the entire genome from nanopore reads using a reference-based…
Answer: Yeast reference-based genome assembly
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The new [hifiassm ONT][1] may be all you need for getting a good assembly. I would not recommend LRSDAY, except for its annotation part (wh…
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Mensur Dlakic
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By the way, these errors are not unique. If you look through the `magpurify` GitHub issues, both types have been reported already.
- https…
Comment: magpurify errors
by
Mensur Dlakic
★
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There is absolutely no chance that a contig labeled `k127_4584534` doesn't exist in your fasta files. These names are not made up out of th…
Comment: magpurify errors
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shevch2009
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Strange but there are no such headers or contig names in my fasta files
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Yes the --prefix Option exists. There is no count per chromosome. You can do it by splitting your input and analyse one sequence at a time…
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You could open a new issue and ask the developers of `maftools` if this was something they can add.
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Do you have the locations/sequence of the regions you are interested in?
Comment: magpurify errors
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Mensur Dlakic
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To me that sounds like an error in sequence header formatting. Maybe some contig headers are repeated? Or their sequences are short or miss…
Comment: magpurify errors
by
shevch2009
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Thanks
What about phylo-markers module error, I tried to look for it :)
But haven't found anything.
And why it's not working for some but …
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