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Compatability with recentrifuge? (add read len to the output)

4

Hi I'm wondering as to the compatability of ganon (classify/report) output with recentrifuge (https://github.com/khyox/recentrifuge/wiki/Running-recentrifuge-for-a-generic-classifier)? I need to remove contaminant reads from the dataset and for a person who doesn't use...

rjsorr

log files

2

I am running ganon (build at present) through a remote connection to a server so I don't always have possibilty to see the screen log. Sometimes the program exits and...

rjsorr

parallelise parse_seqids

1

parse_seqids is called multiple times and is a very slow process. on 57000 unique sequence headers it takes on our system more than 30min. This might be avoidable, if 1)...

oliverdrechsel

Build and classification parameters suggestions based on data type (aDNA)

3

Hi again, another thing that I would absolutely love your input on is build and classification parameters based on the type of data I work with, which is ancient DNA,...

ksavhughes

Output variability between runs/systems?

19

We are in the process in updating nf-core/taxprofiler to include ganon 2.0 During the establishment of CI tests we found there is slight variability in the output (where ganon 1...

jfy133

Clarification questions for kmer/minimizer function

1

I have a few clarifying questions about the kmer/minimizer stuff because it keeps tripping me up. Correct me if I am wrong, but how I picture the kmer/window size thing...

ksavhughes

Estimating and reducing memory usage during build-custom

4

Hello, I've been trying unsuccessfully to build a custom Ganon (v2.1.0) database, however, I am running out of memory on the raptor prepare stage on a machine with 512GB RAM....

peterk87

Building a database for Eukaryotes and others

3

Hi, Thank you very much for creating a good tool Ganon, I am using Ganon for taxonomic profiling but my target is not only bacteria and viruses, but also to...

nvhphuc1206