site_instrument_inventory.md

Sequencing instruments inventory

Document describing each sites sequencing instrument inventory. The document will be used to guide the construction of singulaity images intended to be used to collect and format run data and stats prior to lake upload.

Contributors are free to edit the layout and content of the document as they see fit.

Gothenburg, Clinical Genomics

Gothenburg has both Illumina and Ion torrent machines in clinical use. Not all listed instruments are used for clinical purposes. Below are listed all instruments currently connected to Clinical Genomics Gothenburgs workcluster.

Illumina

Instrument	bcl2fastq	Notes
Novaseq	2.20
Nextseq	2.17	Crashes with bcl2fastq 2.20
Miseq x 3	N/A

Ion Torrent

Instrument	TorrentSuite	Notes
S5 x 2	5.12
PGM	5.12

One S5 is used by the microbiology department for their clinical NGS. The PGM is also used by the microbiology department but does not produce clinical data at the moment.

Stockholm, Clinical Genomics

Illumina

Instrument	bcl2fastq	Notes
Novaseq	2.20	Most commonly used
iSeq	2.20
HiSeq 2500	1.8.4
HiSeq X	2.15

Oxford Nanopore

Instrument	Notes
Flongle	High microbial relevance

Örebro, Clinical Genomics

Illumina

Instrument	bcl2fastq	Notes
NextSeq	2.20
MiSeq

Thermo Fisher

Instrument	Notes
Ion S5

Oxford Nanopore

Instrument	Notes
MinION