Ali May

I suggest waiting for the answer of developers but I’m not sure if Hinge, which is designed for bacterial genomes, is the best option for you. I strongly suggest looking...

Hi Ilan, I'm glad to hear that you see some potential in the CCS assembly idea. Unfortunately I cannot share the data as it belongs to commercial companies (if I...

Thanks a lot for the tips Ilan. I've done some tests with the new parameter set using i) Sequel CCS reads and ii) low-coverage Sequel data (subreads). There is significant...

Thanks a lot for your message Govinda. I don't necessarily need fastg, but since I use spades for short-read assembly, it would be nice to have a graph representation similar...

I get the same error with `hinge clip` **Edit: I cannot reproduce the problem with the HINGE version I built on 2017-08-29. It can only reproduce it with my most...

Hi Govinda, it seems like it worked, I'll let you know after I have a more thorough evaluation. By the way, what I also realised is the huge number of...

I'm getting this error almost certainly when I run workflows where more samples (e.g. 96) than usual are scattered. Cromwell version: 60-6048d0e-SNAP. Is there a workaround to this?

I don't think it's clusterProfiler related, but KEGG related. It looks like it's because of the expired SSL certificate of rest.kegg.jp  when I visit https://rest.kegg.jp/link/ko/pathway, I get  Hopefully...

@nick-youngblut , sure ``` ~/packages/kraken2/build/kraken2 --threads 12 \ > --confidence 0 \ > --unclassified-out HAV1804-11-8-18_39-A_S8_unclassified_R#.fastq.gz \ > --output HAV1804-11-8-18_39-A_S8_kraken_output \ > --report HAV1804-11-8-18_39-A_S8_kraken_report.txt \ > --memory-mapping \ > --use-names \...

@nick-youngblut yes! Also, I do get added reads with Bracken when I use the struo1 database (with lower % of Kraken2-classified reads, of course). Can you confirm that you get...