Michał T. Lorenc

1. What alternatives to JVM do you consider? 2. What do you mean by splitting the project up?

I've never heard before of blaze graph database, but what would you think about elasticsearch database which comes with Full-Text search and could be used for example to find gene...

Good news, thanks to the [Netbeans developer](https://issues.apache.org/jira/browse/NETBEANS-4124) it is possible to use also OpenJDK-13 with Grandle and Groovy within Netbeans. I like Pycharm and [kite](https://kite.com/) extension but they work for...

By any chance, do you know when will you make your final decision about the future of this project?

Hi Mohamed, I add the above pipeline into the original code but I ran into a problem. The code can be found as PR [here](https://github.com/sanger-pathogens/circlator/pull/138). Michal

What is the best way to downsample the short reads to 30X? Thank you in advance, Michal

The reference is a plant genome and to assembled it we used for it PacBio and Hi-C data. On the other hand, the 'Contigs.txt` is a pure 50x Illumina assembly...

Hi, I think the problem was that the assembly contains many small contigs which could not have been assigned to the reference. Additionally, I asked Ragoo to put 100 N's...

Hi, I would be interested in visualising structural variation from Ragoo's output. Thank you in advance, Michal

Hi, I was able to get Assemblytics running with: ``` > cd ragoo_output/ > gzip pm_alignments/pm_against_ref.sam.delta Upload the gz file to http://assemblytics.com/ ``` However, does RaGOO has any script for...