Aldert Zomer

icon indicating an email [email protected]

icon company Utrecht University icon location Utrecht icon location Associate Professor at Utrecht University, Department of Infectious Diseases & Immunology. (meta)genomes, AMR, zoonotic bugs.

Results 4 issues of Aldert Zomer

Can I use databases build with Kraken2

4 comment

To use an existing database, does it have to be a kraken database or can I also use a kraken2 database? build_taxdb works, but krakenuniq generates the error: database ("./bacteria")...

enhancement

.fna files

Often files have the .fna extension. We should recognize these as well as valid sequence files

enhancement

building on Ubuntu 18.04 fails

4 comment

When building I get the following error which is related to math.h /cmath . How do I fix this? CC sources/sequence.cpp => objs/./sources/sequence.o In file included from sources/sequence.h:5:0, from sources/sequence.cpp:1:...

ignoring sequences ending with the same numbers as the reference genome

1 comment

I noticed this odd little bug in parsnp v1.2. When running parsnp using the -c -d options and a reference ending with numbers, genomes that have names that are contained...