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I'm working on a very large genome (4.5 G), when we run medaka, we gets the following error which seems to be related to bam indexing process because of the large genome, I know it would work with sam…
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Hello,
I have a highly hybrid plant genome, jellyfish and genomescope is estimated to be 3.44G , 2.87% heterozygosity, but 4.57G in haifiasm assembly. I try to set the value of --hom-cov 24, he geno…
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First, a suggestion: It would be very helpful to be able to turn off the screen output. We use fastANI with a single query genome against a long list (thousands) of reference genomes (--refList option…
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This produces the expected output:
```R
pdf("test.pdf",
width = 11, # The width of the plot in inches
height = 8.5 # The height of the plot in inches
)
circos.initializeCircularGen…
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Hi there!
I was looking for some feedback using wfmash to align some large (>6gb) plant genomes that are super repeat-dense, around 90%. I was able to make an alignment between species successfully (…
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Hi,
I'm working on annotating a large genome with three chromosomes ranging between 2 and 2.5 Gb in size. Can BRAKER handle chromosomes of this scale?
Thanks in advance.
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Is reveal capable of generating whole genome alignments for multi-gigabase genomes?
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Hi,
Thank you very much for developing this tool!
I find some regions motif edit distance is too large:
`chr1 7105232 7105273 GAGCTGG,GAGCCAA,GGGCTGG,GAGCTGC,GAGCTCT,GAGCTG`
"GAGCTGG","GAGCCAA"…
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Hello,
Curious if you have tested CoreDetector using repeat unmasked version of large plant genomes?
Kind regards,
B
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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…