Martin Hölzer

@Juke34 thanks a lot for looking into this and for the script! I think that's a really good starting point. In this example, I just used a publicly available _Chlamydia_...

@Juke34 I am just finding some time to coming back to this issue and testing your script (once again, thanks a lot!). One question, your command is: ``` agat_sp_prokka_fix_fragmented_gene_annotations.pl --gff...

> yes it is > Did I forgot to mention it in the help? > Edit: No I menhtion it ;) > `--db Input Uniprot fasta file used by prokka....

Yes, category 4 and 5! In this context, it might be also interesting to note that there was a bug in VirSorter predicting prophages that are actually longer than the...

True, it's possible to build an own docker image of the current VS master for WtP... but this @replikation and @mult1fractal have to decide ;) Ah and thanks for the...

What I did this night ago was something really simple with a small ruby script: ```ruby #!/usr/bin/env ruby fastq = File.open("\${reads}", 'r') shuffled = File.open("shuffled.fastq", 'w') i = 0 out...

One could also shuffle by preserving the dinucleotide distribution: https://www.biostars.org/p/134467/ using this script for example: https://github.com/wassermanlab/BiasAway/blob/master/altschulEriksonDinuclShuffle.py or using uShuffle https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2375906/ But maybe just implementing my ruby code into a module...

@replikation @Stormrider935 I adjusted the above ruby code a little bit so that it should be copy-pastable as ruby code into a module

same here, the final assembly fasta does not even exist ``` -rw-r--r-- 1 hoelzerm domänen-benutzer 0 Jun 10 09:32 asm.final.ann -rw-r--r-- 1 hoelzerm domänen-benutzer 0 Jun 10 09:32 backbone.01.init.gfa -rw-r--r--...

I added VirMine to the list, just read the paper and sounds interesting