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Hi Dengfeng,
I am using purge_dups to purge a plant genome generated with ~37x coverage of pacbio hifi reads. Cytological estimates for this species put the put the genome size 850Mb, and kmer anal…
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When a genomes has several versions (for instance : GCF_003555505.1&GCA_003555505.2) should we merge the entry in the results of the analysis ?
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I have carried out the following annotation run on ~1000 isolates:
`for i in `more list`; do echo ${i}; prokka ${i} --proteins fm204883.genbank --locustag SEQ --outdir ${i}_prokka_results; done`
T…
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Hi! This might be an Auspice thing, but since I'm using the nextstrain.org/fetch/ function I'll file it here.
### Current Behavior
When I view https://nextstrain.org/fetch/hgwdev.gi.ucsc.edu/~a…
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* pharokka version: 1.2.0
* Python version: Python 3.8.18
* Operating System: Ubuntu 18.04.6
Hi,
I installed pharokka by the command
```
conda install mamba
mamba install -c bioconda phar…
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Hi~
When I run "rdo.mapCor.gcCor = rd.gcCorrect(rdo.mapCor)", I got the error "Error in { : task 1 failed - "non-numeric argument to binary operator".
I downloaded hg19 annotations from https://xfer…
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Hi Christian,
I've encountered a primary issue while working with the genus Streptococcus and its bacteriophages. I have collected 136 bacterial genomes of the Streptococcus genus and 712 annotated…
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Hello,
I'm having an issue running this pipeline with a new genome index. This install works very well when aligning to human, but with a STAR index/genome/GTF file for another species it fails afte…
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Hello,
sorry this might be a bit of a dumb question. I've got a series of hal alignments generated through cactus that I'd like to screen for genomic regions under selective pressure.
I've been tryi…
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The genome-nexus-vep supports retrieving VEP annotations by a list of variants in **ENSEMBL region** format only.
There is no endpoint to do it by a list of variants in **hgvs** format at the moment.…