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Hi, thanks for your hic integration work to make phasing much easier especially in animal genome assembly. I have run a number of mamal genome assemblies under this mode. Most of the assemblies have a…
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Tool_id toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2
MTS https://toolshed.g2.bx.psu.edu/repository?repository_id=5a89a0b3ecd57228
Install at ORG
EU and AU currently host it.
http…
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The reason multiple insert libraries are used is to strike a balance between long and short range information. Long-insert mate pair libraries are great at telling you two contigs are linked but doesn…
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In the Limitations section you write.
- Minimap2 often misses small exons.
Can you define "small exons"? what's the range? there are exons of 3 bps just to be clear.
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Hi,
I'm trying to do a binning with metabat2 using the following config.yaml:
# ------ Samples ------
samples: '*' # specify a list samples to use or '*' to use all samples
# ------ Resources …
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Hi @fenderglass,
I've adopted a strategy using Illumina reads alongside ONT R10 data to construct and evaluate phased genome assemblies. After assembling with `canu`, I followed with `purged_dups`…
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This is the code they used in `CAMI II`
```
metaquast -r /path/to/set0-9/ref-genomes \
-t 24 --unique-mapping --no-icarus -o /path/to/output_dir \
-l megahit-103-df,megahit-113-df,megahit…
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### Samples
- **SampleID**: _Abundance i wanted to generate_...
- **Size(Gb)**: Amount of bases generated
- **Tot.Reads**: Number of + and - reads generated summed
- **host.reads**: Number of + an…
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Hi vamb devs,
I have some small questions regarding the benchmarking in the vamb publication. I know this work was probably some years back and details blur. Hopefully I'm not bothering you too muc…
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# Final approach before data analysis
## Objective
The main objective of this study is to demonstrate a correlation between high levels of host contamination (HC) and poor assembly and binning per…