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Hi, Thanks for writing such a complete MAN page! I have a quick question, I have a total of 6 samples, and all of them are single cell Nanopore libraries. I'd like both the transcript and gene quantif…
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Hello,
I am using docker command first time, so not much aware of it, i am trying to run deepvariant, tried out almost all possible method to make changes in my command, but i might be missing some m…
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Hi,
I found this post a bit randomly but I found it quite interesting. I'd suggest adding [Spring](https://github.com/shubhamchandak94/Spring) if there is a plan to make another iteration in the fu…
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Hello,
I would like to simulate ONT rolling circle amplification data. Can the NanoSim software be used for this purpose?
Best wishes,
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Hi!
I'm planning to calculate the abundance of MAGs, but I don't know whether the assembly method will affect the command and input data of CoverM. By the way, I use nanopore reads and Illumina reads…
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Hi,
The medaka models used for hybracter only seem to pull v4.2.0 models, when my basecalling has been run using v4.3.0 models
I know that I likely don't need medaka (I turn it off) due to my qua…
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I've been asking for dorado benchmarks so I thought I'd contribute one too. I just put together a system with an AMD 7975X CPU, ASUS WRX90E motherboard, DDR5 memory, Sabrent 8TB SSD and an NVidia RTX …
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Dear all,
I am trying to use vg construct to make a vgraph from a genome (bgzipped and samtools faidxed fasta file) and a variant file (gzipped and tabixed vcf file).
I am using vg version v1.17…
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**Question or Expected behavior**
Genome assembly of the autotetraploid plant
Hi, I have recently assembled a genome using nanopore reads, but the results are not good. It may result from its autot…
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Hello,
I am trying to run Donut Falls with the Unicycler assembler for some ONT and Illumina reads.
I am using the following run command:
`/Shared/SHL-BUG/software/nextflow/nextflow run UPHL-Bio…