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Hello,
Would be possible to perform a SNP variant calling using Nanopore sequencing data? What parameters would have to be modified and how could a custom error model based on Nanopore be created?…
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Hi guys,
Amazing tools!
Are there any plans to include functionality in `bam2pat` to handle nanopre modbams with MM and ML tags? If not, what could be a good way to convert bams with MM and ML t…
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Hi!
Is there a chance it will work with long reads like Nanopore or Pacbio?
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Hello,
I would like to use whatshap polyphase for some samples with ploidy 3. I am using sequence data from Nanopore. The problem is that for SNP calling, the variant callers specific to Nanopore d…
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This code
```console
nextflow run fmalmeida/ngs-preprocess -r dev -latest -profile docker --sra_ids "./input/sra_ids.txt" --output illumina_single --shortreads_type "single" --fastp_addit…
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Good morning,
I am currently using Freebayes ( v1.3.6) to identify variants from Oxford Nanopore sequencing data. However, I have noticed that not all the expected SNPs and insertions are being det…
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Dear author,
Thanks for this pipeline! I am using this pipeline with a mammalian species. I would like to launch the workflow using illumina and nanopore data together. Is it valid to use -sr and -lr…
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Command used:
`
vsnp3_step1.py \
-r1 "$r1" \
--spoligo \
--nanopore
`
Error message:
`
Traceback (most recent call last):
File "/home/bioinfo/miniconda3/envs/vsnp…
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Hi,
is this pipeline suited for nanopore data?
kind regards,
T.
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Hi, this looks interesting.
Is there any reason the tool would not work for nanopore data called by Megalodon (rerio) and modbam2bed ?
i.e. is it restricted to illumina bisulfite data?
Thanks…