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Dear developers,
Thanks for the very nice tool! I have some questions about using HapDup. Could you please give me some hints?
(1) In the readme file, it mentioned that the alignment of reads a…
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Hello, I'm using canu 1.8 to correct my Ustilago maydis reads, I'm using oxford nanopore reads. The correction failed and the error message says the following:
```--
-- ERROR: Read coverage (0) i…
Iseez updated
2 years ago
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I'd like to add an handlegraph interface to get at the GBWTmetadata, like sample and haplotype. This would be useful for reading gbz/gbwt, but also for going back and forth between other formats. It…
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Using a conventional installation (under conda), the first part, getting the code, goes smoothly.
```
git clone --recursive https://github.com/jts/nanopolish.git
Cloning into 'nanopolish'...
remot…
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Here is the canu.out info:
```
-- CONFIGURE CANU
--
-- Detected Java(TM) Runtime Environment '14.0.2' (from '/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/java/14.0.2/bin/java') withou…
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I had a question regarding using WhatsHap to phase PacBio Hifi long reads after using both DeepVariant and GATK for the variant calling.
I was making a trial to see if there would be a difference b…
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Hi,
I have two-run with the same _Anopheles stephensi_ sequencing data with canu v2.2 and canu v1.9. I'm wondering is there any way to check which result is better? I suppose the reads from parental …
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Hi @arangrhie,
I got `Merqury` to work and obtained fairly good results for my human individuals. However, other than the standard plots how can I get the blob plots showing the "correctness" for t…
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Hi,
There are examples for MAGIC in the article, but I did not find usage in the software.
Can mppr be used in the MAGIC.
“An IBD‑based mixed model approach for QTL mapping in multiparental popula…
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Hello,
I ran hicanu (canu 2.2) in a cluster (USDA ARS ceres) with 67x hifi sequences for a 2.4 gb genome assembly. The command is:
canu -p bct -d canu_default genomeSize=2.4g \
batMemor…