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Hello,
Our lab has been using hifiasm for a number of genome assembly projects. We are using Nanopore reads (kit 14 chemistry, R10.4.1 flow cells) that have been error-corrected with PECAT or HERRO…
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I submitted this issue previously [here](https://github.com/schatzlab/genomescope/issues/126) and am following up.
I have now performed kmer counts using Meryl on ccs output from my PacBio HiFi ru…
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Hi,
I'm running variant calling on non-model organisms, and for some of the downstream analyses (e.g., nucleotide diversity calculations), it is necessary to generate (possibly boolean) accessibili…
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Hi, @eblerjana
I found that several samples's peak is wrong according the pangenie log. So would you mind teliing what's the influence of these peak? Is there any way to set peak?
Here is a ex…
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Hello,
I am currently with 92x genome coverage (with pacbio reads) and successfully predicted the 6mA and 4mC positions on the genome (running ipdSummary with the "--identify m6A,m4C" flag).
I wonder …
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Hi!
I'm going to use hifiasm on HiFi data (100x coverage) from an individually amplified worm. I have a previous genome assembly version but would like to redo it with the HiFi. Also, I expect it t…
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I tried to run tophat v2.1.1 with bowtie v1.2.2.0 and got error messages like this.
```
[2018-01-20 20:30:21] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-01…
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Hello,
I am currelty running insilicoseq_1.5.3 to generate simulated reads from the mm39 mouse genome. I am running the program using the coverage_file option with a 30 coverage in chr1-19 and once …
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### Description of bug
I am using Spades for genome assembly of Illumina PE data and while it runs great to completion on each job I've done, I'm finding there is an inflection point in genome cove…
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Hello dear developers,
I am using PECAT to assemble a diploid genome (SMRT Cell, PacBio), however, the process is stuck at the assembly stage, the following error appears:
```
2024-07-31 11:0…