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Hi,
I have just started learning bowtie2. I encountered a problem with database indexing with bowtie2-build command: indexing runs through but the output doesn't have .rev files, thus preventing me…
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Thanks for the nice tool! Is it possible for this tool run against the customed microbial genomes?
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Dear SURPIrt-dist Developers,
It is not clear from README files how to regenerate the reference databases used by SURPIrt for identification of human, bacterial, fungal, and parasitic reads and for…
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Hello! I'm currently trying to run a gapped alignment with the mmseqs search function, but I can't find an appropriate parameter to do this. I'm attempting to look for an individual query gene in a da…
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Hi @ajkarloss
Thanks for the tool plasmidfinder.
I am developing a nextflow pipeline to assemble multiple bacterial genomes using long read (ONT) read. I want to apply your tool plasmidfinder t…
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I recently updated my nr and krona tools databases and when I used ktClassifyBLAST to classify my blast results I got a warning that hundreds of accession numbers were not found in my local database. …
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Hi, I have downloaded 'bacteria' library by typing "kraken2-build --download-library bacteria --db $DBNAME". and I found it's pretty large in size, around 81GB. I'm not sure if that's OK and how much …
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Trying to understand a discrepancy between my much loved mlst vs CGE webtool (https://cge.cbs.dtu.dk/services/).
I have an isolate of S.suis, sequenced with Illumina > denovo assembled contigs gene…
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In https://github.com/ekg/freebayes/issues/419 @tseemann [asked if vg was ready for bacterial pangenomics](https://github.com/ekg/freebayes/issues/419#issuecomment-377646948). My response better fits …
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Motivation: I have colleagues who would like to use this tool, but for more than just generating taxonomic profiles. I would also like to utilize the resulting SAM files to do things like investigate …