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I ran jellyfish count on ccs reads produced from PacBio HiFi sequencing as follows:
```
jellyfish count -C -m 31 -s 1000 -t 10 -o marten.pb.jf m64047_240219_192555.ccs.fasta
```
And subsequent…
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We ran a full-length Pacbio DADA2 analysis. Here is a question we encountered during the process:
There is some minor read loss during the DADA2 process. For example, in one sample, stats.tsv shows 2…
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Hi,
What would be your recommended parameters to map corrected pacbio reads (after 1 step of canu for example) against a genome ?
This will be used for inversion detection (with sniffles or/and …
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Hi, I ran this command to perform Isoquant quantification with the aim of obtaining transcript quantification results for all samples: isoquant.py --reference genome.fa --genedb ./merge.combined.gtf -…
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We're seeing some fragmentation on workflows due to switches in technologies (PacBio, Shoreline, Loop, etc) that a migration to DSL2 would help tremendously. This is a simple tracker to plot a course…
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Hi!
I'm trying to us ntJoin to scaffold an input PacBio CLR genome assembly using a chromosome level assembly of a closely related species as a refence.
1) I would like to ask what's best? Use t…
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Hi,
This is a very promising tool, thank you for writing it! I have a question about error profiles. The pacbio CCS error profile didn't look much different from the RSII / sequel2 (especially fo…
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Thanks for providing and maintaining HASLR. Is it possible to use HASLR to assembly sequences from pacbio, nanopore, and Illumina all together at the same time? I have used HASLR to assembly pacbio …
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Hi, anyone is interested in aligning PacBio reads to assembly graph? I tried few examples, it looks vg does not do the right thing. Here are the listed things:
1. align pacbio reads to assembly (base…
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Hello,
I downloaded the binary version of bwa-mem2 (v2.2) on my server and I try to run bwa-mem2 but I get a segmentation fault.
My linux distribution is **Scientific Linux release 6.9 (Carbon)*…