Bioinformatics inventory 2024

Bioinformatics pipeline inventory

Done in March 2024

Pipeline	Description	Note	Clinical/Research
nf-core/taxprofiler	Shotgun metagenomics	In validation	Both
in-house sars cov wrapper	wrapper around artic, Sars-CoV-2 typing		Clinical
HICCOP	Hiv typing	In use	Clinical
hcv resfind	HCV resistance profiling	In use	Clinical
cmv resfind	CMV resistance profiling	In use	Clinical
MRSA typefind	MRSA typing	In use	Clinical
HBV pipeline	HBV resistance typing	In validation	Clinical

Pipeline	Description	Note	Clinical/Research
nf-core/taxprofiler	Shotgun metagenomics	In clinical validation	Clinical
GMS_16S	16S metagenomics	Interesting in the future	Clinical
in-house SARS-CoV-2	SARS-CoV-2 typing	In use (will be replaced by upload to Gensam in 2024)	Clinical
in-house Bacterial WGS typing	Species ID, MLST, spa, gene detection (MRSA, ESBL, VRE, NTM), SNP outbreak analysis	In use	Clinical
in-house TB variants	Resistance (WHO) and lineage	In use	Clinical
in-house NTM variants	Resistance in M. abscessus and M. avium complex	In use	Clinical

Pipeline	Description	Note	Clinical/Research
cmd-job	Bacterial epityping and virulence/amr detection	In house analysis system that is being phased out	Clinical
sarscov2-pipe/sc2reporter	Sars-CoV-2 typing and visualisation	In house	Clinical
jasen/bonsai	bacterial typing and visualisation	primary analysis for TB and MRSA from Q2 (more later 2024)	Clinical
gms_16S	16S metagenomics	16S is in transitioning phase from Sanger	Clinical

Pipeline	Description	Note	Clinical/Research
microSALT	Microbial WGS eppityping and resistance gene detection	Will be replaced with JASEN (Q2 2024)	Both
nf-core/taxprofiler	Shotgun metagenomics		Both
MUTANT	Sars-CoV-2 typing	Wrapper on GMS-Artic	Clinical
Time pipeline	Determining time of HIV infection		Research
GMS_16S	16S metagenomics	Not implemented yet	Clinical

Pipeline	Description	Note	Clinical/Research
epi2me-labs/wf-artic	SARS-CoV-2 typing	in use	clinical

Pipeline	Description	Note	Clinical/Research
in-house pipeline	SARS-CoV-2 typing (Geneious workflow)	in use	Both
in-house pipeline	16S (Geneious workflow with emu)	in validation	Both

Pipeline	Description	Note	Clinical/Research
nf-core/taxprofiler	shotgun metagenomics	Implemented	Research
JASEN	Bacterial typing	Not implemented
GMS_16S	16S metagenomics	Implemented	Research
Ridom SeqSphere+	MRSA, MC	Implemented	Clinical
1928 Diagnostics	MRSA, 16S, VRE,C.Diff	Implemented	Clinical
CLC Genomics Workbench	GC-typing	Implemented	Clinical
PubMLST/BIGSdb	MC	Implemented	Clinical
GMS Artic	SARS-CoV-2	Implemented	Clinical (not in use)