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I just took a quick look at your fastq files in the `fastq-spragueuBiomeJan2015` folder. A couple things jump out at me...
1. Do you know which body sites these are for? Does each lane's worth of dat…
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**All twister tests fail when using the Cadence toolchain on the qemu_xtensa platform**
SOF is built for Xtensa using the Cadence toolchain, for consistency it should also be possible to use it to ru…
lyakh updated
3 weeks ago
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Hi:
I'm looking at gene rearrangement in the neighbourhood flanking a single core block in related plasmid sequences - when the core block is oriented in the strand=+ direction, the sequence is cor…
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It is taking around 4-5 hours to run on one exome VCF of around 90K variants
(running on Xeon 32 core processor + 120Gb Ram workstation)
Is it normal run time you expect?
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**Describe the bug**
VariantValidator provides incorrect HGVS descriptions for intronic variants. E.g.,
- [`NM_001283009.2:c.1266+3_1266+80del`](https://variantvalidator.org/service/validate/?varian…
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Hi,
If I have a series of interchromosomal translocation events stored in .vcf file, can I construct a graph that represent this kind of variants using vg ? If vg cannot solve this problem, can o…
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- Two main data generation strategies: (1) amplicon sequencing and (2) shotgun sequencing
- At this time analysis one can choose calling variants or performing within-host evolution analyses inclu…
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Hello,
First of all: thank you very much for the pipeline.
I ran the command like this:
nextflow run cgroza/GraffiTE --assemblies assemblies.csv --TE_library nrTREP20 --reference Bgt_genome_v…
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I'm not sure whether `Whatshap` can be used to phase SVs. I tried it but some reads were not phased correctly. Ideally my reads should be phased into two haplotypes: one containing a ~5640bp insertion…
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Hi, here are several issues i found with the designation and topology of several variants :
DV.8 is seemed to evolve out of DV.1 and not from it’s parent CH.1.1.1
https://nextstrain.org/fetch/geno…