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Hi Dr. Shujun,
EDTA is a very good software!
Recently, I also encountered a problem when annotating TE sequences in the IWGSCv1p1A.fa genome with EDTA. The error message is as follows: No SINE res…
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Hi Brian,
We recently stumbled on some ab initio gene prediction issues with large genomes. After reducing the individual chromosome sizes (some were >2Gb) we could continue with some of these tool…
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Dear yupenghe,
I would like to know to deal with organisms that have chromosomes more than 512Mb.
During mapping, samtools index command failed with showing the error message.
`samtools index: fa…
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Dear authors,
We have a genome about 5G, and the amount of HIFI data is about 134G. We want to get a better preliminary assembly result with hifiasm software with the default parameter: hifiasm - o …
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Reference to issues [here ](https://github.com/lh3/minimap2/issues/58)
Minimap multi-part index doesn't output SQ fields
Options: check if mapping can be run without index output ```-d```.
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Hello again, Bogdan and Michael,
So far, `make_lastz_chains` has been working great, and the largest successfully aligned was the wheat genome (14.6 Gb). This time, I was asked to see if [the lung…
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Hi!
I found this error (Command terminated by signal 9) when running PGGB, which may be caused by insufficient memory.
I want to know how much memory is needed if I want to use PGGB to construc…
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Hi,
thanks for this nice modern tool. I could install easily via `pixi shell` btw.
I'm wondering if the tool will be fast enough for eukaryotes, eg plants? I saw you've tested on E. coli I think…
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flo failed on a 14Gb genome, with "corrupted double-linked list (not small)" error. it runs normally with genome smaller than 4Gb in size. The setting is on an aws m5.16xlarge EC2 instance.
rake -f…
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There seems to be a large KP.3.1.1+S:S31F branch, while KP.3.1.1 shall have S:31del.
That branch is driven by Denmark seqs which do not handle S:S31del well. When Querying C12616T, A13121T, C2165…