README

Rasmus Kirkegaard 21 November, 2024

MicroBench

Overview of our data for microbial genomic benchmarking. We have sequenced a bunch of mono cultures, and metagenomic samples.

Monocultures:

• Anabaena variabilis PCC 7120 DSM 107007
• Desulfobacca acetoxidans ASRB2 DSM 11109
• Sagittula stellata E-37 DSM 11524
• Salmonella bongori 1224.72 DSM 13772
• Burkholderia cenocepacia J2315 DSM 16553
• Sphaerobacter thermophilus S 6022 DSM 20745
• Zymomonas mobilis subsp. pomaceae Barker I DSM 22645
• Pelobacter carbinolicus Bd1 DSM 2380
• Methanocaldococcus jannaschii JAL-1 DSM 2661
• Sphaerotilus natans 6 DSM 6575
• Thermanaerovibrio acidaminovorans Su883 DSM 6589

Mock Metagenomes:

• ZymoGut
• ZymoHMW
• ZymoOral

“Real” metagenomes:

• ZymoFecal

To do:

• Sequence all standards
• Get AAU to support public links or upload data to NCBI/ENA

Mono cultures

Anabaena variabilis PCC 7120 DSM 107007

You find a description of this sample here: https://www.dsmz.de/collection/catalogue/details/culture/DSM-107007

Sample	date of sequencing	sequencing kit	flowcell type	flowcell ID	sample rate	date of basecalling	dorado version	basecall model version	fast	hac	hacdup	sup	supdup	mods	pod5
Anabaena variabilis PCC 7120 DSM 107007	2024-11-01	SQK-RBK114.24	FLO-PRO114M	PAW78174	5 khz	2024-11-05	0.8.2	5.0.0	fast	hac	NA	sup	NA	NA	pod5

Desulfobacca acetoxidans ASRB2 DSM 11109

You find a description of this sample here: https://www.dsmz.de/collection/catalogue/details/culture/DSM-11109

Sample	date of sequencing	sequencing kit	flowcell type	flowcell ID	sample rate	date of basecalling	dorado version	basecall model version	fast	hac	hacdup	sup	supdup	mods	pod5
Desulfobacca acetoxidans ASRB2 DSM 11109	2024-11-01	SQK-RBK114.24	FLO-PRO114M	PAW78174	5 khz	2024-11-07	0.8.2	5.0.0	fast	hac	NA	sup	NA	NA	pod5

Sagittula stellata E-37 DSM 11524

You find a description of this sample here: https://www.dsmz.de/collection/catalogue/details/culture/DSM-11524

Sample	date of sequencing	sequencing kit	flowcell type	flowcell ID	sample rate	date of basecalling	dorado version	basecall model version	fast	hac	hacdup	sup	supdup	mods	pod5
Sagittula stellata E-37 DSM 11524	2024-11-01	SQK-RBK114.24	FLO-PRO114M	PAW78174	5 khz	2024-11-07	0.8.2	5.0.0	fast	hac	NA	sup	NA	NA	pod5

Salmonella bongori 1224.72 DSM 13772

You find a description of this sample here: https://www.dsmz.de/collection/catalogue/details/culture/DSM-13772

Sample	date of sequencing	sequencing kit	flowcell type	flowcell ID	sample rate	date of basecalling	dorado version	basecall model version	fast	hac	hacdup	sup	supdup	mods	pod5
Salmonella bongori 1224.72 DSM 13772	2024-11-01	SQK-RBK114.24	FLO-PRO114M	PAW78174	5 khz	2024-11-07	0.8.2	5.0.0	fast	hac	NA	sup	NA	NA	pod5

Burkholderia cenocepacia J2315 DSM 16553

You find a description of this sample here: https://www.dsmz.de/collection/catalogue/details/culture/DSM-16553

Sample	date of sequencing	sequencing kit	flowcell type	flowcell ID	sample rate	date of basecalling	dorado version	basecall model version	fast	hac	hacdup	sup	supdup	mods	pod5
Burkholderia cenocepacia J2315 DSM 16553	2024-11-01	SQK-RBK114.24	FLO-PRO114M	PAW78174	5 khz	2024-11-07	0.8.2	5.0.0	fast	hac	NA	sup	NA	NA	pod5

Sphaerobacter thermophilus S 6022 DSM 20745

You find a description of this sample here: https://www.dsmz.de/collection/catalogue/details/culture/DSM-20745

Sample	date of sequencing	sequencing kit	flowcell type	flowcell ID	sample rate	date of basecalling	dorado version	basecall model version	fast	hac	hacdup	sup	supdup	mods	pod5
Sphaerobacter thermophilus S 6022 DSM 20745	2024-11-01	SQK-RBK114.24	FLO-PRO114M	PAW78174	5 khz	2024-11-07	0.8.2	5.0.0	fast	hac	NA	sup	NA	NA	pod5

Zymomonas mobilis subsp. pomaceae Barker I DSM 22645

You find a description of this sample here: https://www.dsmz.de/collection/catalogue/details/culture/DSM-22645

Sample	date of sequencing	sequencing kit	flowcell type	flowcell ID	sample rate	date of basecalling	dorado version	basecall model version	fast	hac	hacdup	sup	supdup	mods	pod5
Zymomonas mobilis subsp. pomaceae Barker I DSM 22645	2024-11-01	SQK-RBK114.24	FLO-PRO114M	PAW78174	5 khz	2024-11-07	0.8.2	5.0.0	fast	hac	NA	sup	NA	NA	pod5

Pelobacter carbinolicus Bd1 DSM 2380

You find a description of this sample here: https://www.dsmz.de/collection/catalogue/details/culture/DSM-2380

Sample	date of sequencing	sequencing kit	flowcell type	flowcell ID	sample rate	date of basecalling	dorado version	basecall model version	fast	hac	hacdup	sup	supdup	mods	pod5
Pelobacter carbinolicus Bd1 DSM 2380	2024-11-01	SQK-RBK114.24	FLO-PRO114M	PAW78174	5 khz	2024-11-07	0.8.2	5.0.0	fast	hac	NA	sup	NA	NA	pod5

Methanocaldococcus jannaschii JAL-1 DSM 2661

You find a description of this sample here: https://www.dsmz.de/collection/catalogue/details/culture/DSM-2661

Sample	date of sequencing	sequencing kit	flowcell type	flowcell ID	sample rate	date of basecalling	dorado version	basecall model version	fast	hac	hacdup	sup	supdup	mods	pod5
Methanocaldococcus jannaschii JAL-1 DSM 2661	2024-11-01	SQK-RBK114.24	FLO-PRO114M	PAW78174	5 khz	2024-11-07	0.8.2	5.0.0	fast	hac	NA	sup	NA	NA	pod5

Sphaerotilus natans 6 DSM 6575

You find a description of this sample here: https://www.dsmz.de/collection/catalogue/details/culture/DSM-6575

Sample	date of sequencing	sequencing kit	flowcell type	flowcell ID	sample rate	date of basecalling	dorado version	basecall model version	fast	hac	hacdup	sup	supdup	mods	pod5
Sphaerotilus natans 6 DSM 6575	2024-11-01	SQK-RBK114.24	FLO-PRO114M	PAW78174	5 khz	2024-11-07	0.8.2	5.0.0	fast	hac	NA	sup	NA	NA	pod5

Thermanaerovibrio acidaminovorans Su883 DSM 6589

You find a description of this sample here: https://www.dsmz.de/collection/catalogue/details/culture/DSM-6589

Sample	date of sequencing	sequencing kit	flowcell type	flowcell ID	sample rate	date of basecalling	dorado version	basecall model version	fast	hac	hacdup	sup	supdup	mods	pod5
Thermanaerovibrio acidaminovorans Su883 DSM 6589	2024-11-01	SQK-RBK114.24	FLO-PRO114M	PAW78174	5 khz	2024-11-07	0.8.2	5.0.0	fast	hac	NA	sup	NA	NA	pod5

Mock metagenomes

ZymoGut

You find a description of this sample here: https://zymoresearch.eu/products/zymobiomics-gut-microbiome-standard

Sample	date of sequencing	sequencing kit	flowcell type	flowcell ID	sample rate	date of basecalling	dorado version	basecall model version	fast	hac	hacdup	sup	supdup	mods	pod5
ZymoGut	2024-10-25	SQK-NBD114.24	FLO-PRO114M	PAY12289	5 khz	2024-10-28	0.8.2	5.0.0	fast	hac	NA	sup	NA	mods	pod5

ZymoHMW

You find a description of this sample here: https://zymoresearch.eu/products/zymobiomics-hmw-dna-standard

Sample	date of sequencing	sequencing kit	flowcell type	flowcell ID	sample rate	date of basecalling	dorado version	basecall model version	fast	hac	hacdup	sup	supdup	mods	pod5
ZymoHMW	2023-08-08	LSK114	FLO-PRO114HD	PAS01578	5 khz	2024-09-13	0.7.3	5.0.0	fast	hac	hacdup	sup	supdup	mods	pod5
ZymoHMW	2023-08-08	LSK114	FLO-PRO114HD	PAS01578	5 khz	2023-12-16	0.3.4	4.2.0	NA	NA	NA	sup	supdup	NA	pod5

ZymoOral

You find a description of this sample here: https://zymoresearch.eu/products/zymobiomics-oral-microbiome-standard

Sample	date of sequencing	sequencing kit	flowcell type	flowcell ID	sample rate	date of basecalling	dorado version	basecall model version	fast	hac	hacdup	sup	supdup	mods	pod5
ZymoOral	2024-10-25	SQK-NBD114.24	FLO-PRO114M	PAY12289	5 khz	2024-10-29	0.8.2	5.0.0	fast	hac	NA	sup	NA	mods	pod5

“Real” metagenomes

ZymoFecal

You find a description of this sample here: https://zymoresearch.eu/collections/zymobiomics-microbial-community-standards/products/zymobiomics-fecal-reference-with-trumatrix-technology

Sample	date of sequencing	sequencing kit	flowcell type	flowcell ID	sample rate	date of basecalling	dorado version	basecall model version	fast	hac	hacdup	sup	supdup	mods	pod5
ZymoFecal	2024-10-01	LSK114	FLO-PRO114M	PAW77640	5 khz	2024-11-08	0.8.2	5.0.0	fast	hac	NA	sup	NA	mods	pod5
ZymoFecal	2024-10-01	LSK114	FLO-PRO114M	PAW77640	5 khz	2024-10-07	0.8.1	5.0.0	NA	NA	NA	NA	NA	NA	pod5
ZymoFecal	2024-10-01	LSK114	FLO-PRO114M	PAW77640	5 khz	2024-10-05	0.7.3	5.0.0	NA	NA	NA	NA	NA	mods	pod5