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Hi,
I successfully assembled an _A. thaliana_ genome for which I obtained two partially phased haplotypes of size 148.1 Mb (hap1) and 146.4 Mb (hap2), respectively. These files are in **.fasta** f…
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@mbhall88 noted a potential problem with the `--max_covg` parameter that can affect `pandora map` and `pandora compare`: unmapped reads enter the coverage calculation although they do not contribute f…
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* contamination (host and non-intentional)
* low read coverage
* diverse organisms
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Hi, I used the nice tool CoverM for calculating the coverage of MAG, but get an error. Please give me some advice, thanks!
Code:
`coverm genome --coupled Reads/BPA_1.fastq Reads/BPA_2.fastq Reads/…
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Hello,
Thanks so much for developing this tool, I find it quite easy to use.
I'm wondering what's causing duplicated transcripts (identical coordinates, different transcript id) to have differen…
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Comparing the result of the consensus, we found that the result was not identical between viridian and our lab-built ivar pipeline on artic V3 protocol.
With viridia, the low depth of coverage regio…
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I'm interested in using pangeo-forge for other types of datasets, specifically genomic datasets. The current set of recipe classes are focused on climate-oriented data formats (netcdf, hdf, zarr). I…
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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…
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I am running nanopolish variant calling on chr22 of a NA12878 dataset. I generated small regions using the *make range script* and launched multiple nanopolish instances using *parallel* command. How…
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I would like to impute the data of another chip in order to get the missing points of the BovineSNP50 chip.
My source data in ped format. I got VCF files using plink1.9 and prepared a reference (~500…