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May `--cov-threshold` be enabled to be multiple integers separated by a comma (and _median_ coverage as another option)?
 for borrowing information from sample-matched whole genome sequencing. Such …
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Hello,
Is the WASP mapping pipeline suitable/recommended to be used on WGS data? I have followed some suggestions here to split some of the steps by chromosome since the files are large. However, f…
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I am currently conducting Whole Genome Bisulfite Sequencing (WGBS) data analysis using Bismark and plan to utilize a soft-masked genome, where all repetitive and low-complexity regions are marked with…
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Hi Juliana, Thank you for sharing your genetic QC pipeline—it has been incredibly helpful. I have a question regarding whole-genome sequencing (WGS) data. Due to its large size, it's often to separate…
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Hi,
I am working on annotating large datasets, specifically Whole Genome Sequencing (WGS) VCF files, using the Variant Effect Predictor (VEP). However, the annotation process is taking significantl…
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Issue by @MaxUlysse, moved from SciLifeLab#666
- [ ] [ExpansionHunter](https://github.com/Illumina/ExpansionHunter) for estimating repeat sizes
- [ ] [QDNAseq](https://github.com/ccagc/QDNAseq) CN…
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Hello,
I'm new to whole genome assembly using ONT reads. I have two questions.
Suppose the consensus sequences identified during the inference are not adapters but are important to the project …