Adrian Fritz

Hey, sorry for not having responded in a while. I have tried a lot to reproduce this problem, but for me - using your config file but the genomes from...

This should be fixed in the later versions of CAMISIM and Nanosim though CIGAR calculation is still deactivated currently. The latest Nanosim version which will be part of the big...

Without more context it is very hard to tell what is going wrong. CAMISIM fails during creation of the binning gold standard of a non-anonymized data set, you could try...

Hm, this is something I have never encountered, it seems CAMISIM fails to remove the temporary files. This makes me think that it might be a problem with permissions -...

Closed due to inactivity

Actually this is possible, yes! You will need to use the `-ar`/`--additional-references` option. This file has to be in a tab-separated format with the 4 columns NCBI_ID Scientific_name genome_path novelty_category...

You don't need to provide these NCBI IDs then, so yes it could look like this, though just to be safe I'd advise using absolute paths to your genomes.

Actually, looking at the code right now I was mistaken. For CAMISIM to work, every entry in the reference file needs to have a "correct" NCBI ID and scientific name,...

Since you do not use CAMISIM's option to download genomes the _de novo_ design might actually be best (and more accurate). To use the abundances from the input profile you...

No, you should not need to change the phase, CAMISIM will automatically use the files if they are provided. Note that for multiple samples these need to be absolute paths...