Daniel Anderson

icon company European Bioinformatics Institute icon location Hinxton, United Kingdom icon location PhD student at EMBL-EBI & The University of Cambridge.

Results 4 comments of Daniel Anderson

Pandora mapping is slow

This is correct, I will try to make plots of runtime vs number of reads after I have looked at the gene calling in more detail- without lazy loading the...

Error: Prefilter & Search step died with mmseqs 15.6f452 easy-cluster

This issue seems to come up fairly regularly so for anyone looking for a solution, mmseqs v14.7e284 worked on these sequences for me.

Panaroo reporting genes of very different lengths together in the same gene family - Expected Behaviour?

Hi @NickJD, are you running panaroo using the default parameters? If so see #300.

0 depth reported across many genes in the pandora consensus

Apologies I realise I never actually collected an example of this happening. From my recollection it happens pretty frequently though, like multiple times per sample. On 8 Sep 2025, at...