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Hello, I have a question regarding application of Bowtie2 for metagenomics data.
I have created a reference fasta file with a list of 10 viruses of interest.
Lets say I take one input sample co…
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the program was working well but today I reinstalled on a different machine and whenever I run it on fastq samples, I got this "NO high coverage Kmer found"
previously on the same samples, the prog…
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I am running poppunk on a large set of sequences that essentially lack any accessory gene content. I can complete the first step fo generating the DB, but when trying to run an initial model fit, I g…
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Hi!
First, congrats for your work on Ra and Raven. I've been following and testing your work for nanopore reads for quite a while.
I work in viral genomics (dsDNA viruses), studying new viruses,…
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Hi Eric,
I hope this finds you well. I tried running VADR on the SARS-CoV-2 reference genome from NCBI, and against a distantly-related CoV genome that we found:
https://github.com/ababaian/serr…
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Hello,
I am attempting to build a custom (standard plus fungi) kraken2 database and keep getting a timeout error. I wanted to ask if others have seen this before and had any suggestions?
I look…
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While trying to calculate a comparison to the sketchlib output (which worked fine with the same input seconds previously, in easy-run mode), I encountered this error - seems like there might be an iss…
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Per [ICTV](https://talk.ictvonline.org/ictv-reports/ictv_9th_report/positive-sense-rna-viruses-2011/w/posrna_viruses/222/coronaviridae) "[Corona]viruses that share more than 90% aa sequence identity i…
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Hi!
I use DRAM in an conda environment, this is my command line:
`DRAM.py annotate -i '/home/awerner/OMZ/7494_fa/*.fa' -o /home/awerner/OMZ/DRAM/annotation_out --threads 10 `
For one of the seq…
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Hi,
I would like to use snpEff to annotate the variations in to synonymous non-synonymous mutations and to see the animo acid change caused by the mutations. I built the Pseudomonas phage phi-2 [(…