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First of all, thank you for providing such an excellent tool for TE annotation. I’m currently using EDTA v2.2.1 to annotate transposable elements for a large genome, GCA_014155895.2 (~16G). Due to its…
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Hello @chhylp123
I used hifiasm in trio binning mode using Illumina reads from the parents and HiFi reads from the hybrid. The resulting assemblies (hap1 and hap2) have high duplication levels and…
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Hello,
I am trying to use purge_dupes on my Nanopore-based genome assembly. Heterozygosity is estimated (using GenomeScope and Illumina data) to be ~3% in this organism, which has a 1C genome size of…
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**Is your feature request related to a problem? Please describe.**
Many wastewater surveillance groups do not have access to hospitalization data and/or access to hospitalization data at the same spa…
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Thanks for developing the easy use software!
We found the genome size estimate of our arthropod assembly was quite dependent the max k-mer coverage . The genome size is 30% larger after increasing…
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Hello,
I am using the latest version of the pipeline (v.1.0.3) and I am testing a large group of genomes from ncbi (very variable in quality) using the profile module both with PROT and BUSCO.
For…
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We routinely use Minimap2 for processing large nanopore sequencing datasets which take hours. For example, aligning a single 30x dataset to the human genome using Minimap2 takes approximately 12 hours…
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Hi - Thanks for developing this tool.
Just wondering if there's a way to get genotypes. We are comparing alignments of several individuals to our reference and would like to get an idea how the SVs…
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It's not listed at https://useast.ensembl.org/info/genome/variation/predicted_data.html#consequences but it still shows up in the results of a large project. vcf2maf assigns it the lowest priority by …
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Hello, thank you for this pipeline that seems very interesting !
I have 3 questions :
- About the input files, especially the "gc" and "mappability" bed files. It's the first package I find that…