JohnVollmers

Hi ralf, This is probably too late and I am not involved in the development of megahit in any way, but i think i may have an idea what could...

Hmm, from what i can gather, plass should be suitable for functional gene analysis. But for your potential follow-up (reconstructing MAGs) you will probably have to fall back on megahit...

in that case i would still recommend merging the reads first (it should significantly enhance the likelyhood to assembly very low abundant genome fragments). But of course this would only...

Well, the numbers from the trial above are skewed and not really comparable. for the run withut read merging, you only output contigs that were assembled beyond the single read...

Well, but if the main concern here also is that users don't read the manual, shouldn't that be even more a reason to choose a safe default value over a...

That would add some safety at least, if setting default to 1 is not an option. Perhaps even kill\abort itself if the load exceeds the available CPUs? Or one could...

I would like to mention here that sometimes I like to use genbank_get_genomes_by_taxon.py to gather reference genomes for larger taxonomic groups (sometimes up to phylum-level). Especially in cases where clinically...

Hi, yes I also found that the type strains are not necessarily actually representative for a species. Often they were just the first or most easy to Isolate. It's just...

Well, DID you run updateTaxonomy.sh? It should download the taxonomy information from NCBI. That should create a file "taxonomy.tab" in the directory ```/Users/LibethSanchez/krona/Krona-master/KronaTools/taxonomy```. If ```updateTaxonomy.sh``` is not in your PATH,...

similar problem here. Installing from conda works. So thats good, already. But installing without conda does not seem to work, even WHEN capnp is installed. Trying to instalI without conda...