UMGC Sequencer Home


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2	High-output HiSeq 2500 ("Franklin") Run Calendar				Last updated on 08/17/2017. Questions? E-mail: next-gen@umn.edu
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4	Flow cell position: A		Flow cell position: B		This is a web-published Google Sheet best viewed using Google Chrome or Apple Safari browsers. Firefox is not recommended.
5	Idle		Idle
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7	Current Run in Position A		Current Run in Position B
8	Start	8/16/2017	Start
9	End	8/23/2017	End
10	Elapsed	Has been running for 6 days.	Elapsed
11	Run Type	2x125-bp Paired-End DI	Run Type
12	Run ID	HS4_FC_A_08_15_17	Run ID
13	Lane 1	Sadowsky_151	Lane 1
14	Lane 2	Harris_081	Lane 2
15	Lane 3	Harris_081	Lane 3
16	Lane 4	Harris_081	Lane 4
17	Lane 5	Harris_081	Lane 5
18	Lane 6	Harris_081 (0.5) Riehle_002 Reseq (0.1)	Lane 6
19	Lane 7	Springer_055	Lane 7
20	Lane 8	Springer_055	Lane 8
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22	Queued Run A1		Queued Run B1
23	Est'd Start	8/23/2017	Est'd Start	8/21/2017
24	Est'd End	8/28/2017	Est'd End	8/23/2017
25	Run Type	2x50-bp Paired End DI	Run Type	1x50-bp Single Read DI
26	Lane 1	Kobayashi2_002	Lane 1	Jameson_011
27	Lane 2	Kobayashi2_002	Lane 2	Finno_012
28	Lane 3	Kobayashi2_002	Lane 3	Finno_012
29	Lane 4	Marchant_004 (0.5) Starr_039 (0.5)	Lane 4	Finno_012
30	Lane 5	Schmidt_033	Lane 5	Finno_012
31	Lane 6	Dunny_036	Lane 6	Finno_012
32	Lane 7	Largaespada_116	Lane 7	Masopust_011
33	Lane 8	Ward2_004 Pool 1	Lane 8	Langlois_006
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35	Queued Run A2		Queued Run B2
36	Est'd Start	8/29/2017	Est'd Start	8/23/2017
37	Est'd End	9/5/2017	Est'd End	8/28/2017
38	Run Type	2x125-bp Paired-End DI	Run Type	2x125-bp Paired-End DI
39	Lane 1	Peatman_002	Lane 1	UMGC_434 (Clinical Whole Exome)
40	Lane 2	Arbefeville_001/002	Lane 2	UMGC_434
41	Lane 3	Harris_Project_076 QXT	Lane 3	UMGC_436 (Trusight 2 Validation)
42	Lane 4	Harris_Project_076 QXT	Lane 4	UMGC_436
43	Lane 5	Harris_Project_076 QXT (0.5) Baughn_015 Repool (0.5)	Lane 5	UMGC_436
44	Lane 6	Orr_029	Lane 6	UMGC_436
45	Lane 7	Orr_029	Lane 7	UMGC_436
46	Lane 8	Orr_029	Lane 8	UMGC_436
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48	Queued Run A3		Queued Run B3
49	Est'd Start	9/5/2017	Est'd Start	8/25/2017
50	Est'd End	9/12/2017	Est'd End	8/29/2017
51	Run Type	2x125-bp Paired-End DI	Run Type	2x50-bp Paired End DI
52	Lane 1	Vernick2_020	Lane 1	Duan_005
53	Lane 2	Vernick2_020	Lane 2	Duan_005
54	Lane 3	Marks_032	Lane 3	Duan_005
55	Lane 4	Marks_032	Lane 4	Duan_005
56	Lane 5	Marks_032	Lane 5	Duan_005
57	Lane 6	Novak_006	Lane 6	Duan_005
58	Lane 7		Lane 7	Duan_005
59	Lane 8		Lane 8	Duan_005


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2	HiSeq 2500 High-output Sample Queue (Samples being readied for sequencing on "Franklin").												Last updated on 9/28/2016 by Elyse Froehling (escooper@umn.edu)
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4	1x50 bp Single Read Libraries						2x50 Paired-end Libraries						This is a web-published Google Sheet best viewed using Google Chrome or Apple Safari browsers. Firefox is not recommended.
5	Investigator	# of Lanes	Library Status (Est'd Date)	Queued Run Name	# Lanes Filled	Estimated Run Date	Investigator	# of Lanes	Library Status (Est'd Date)	Queued Run Name	# Lanes Filled	Estimated Run Date	Explainer
6	Finno_012	5	7/30/2017				Nakato_003	1	7/26/17	B1			The tables on the left report currently sequencing -- and future -- high-output sequencing libraries. The availability of libraries determines the timing of queued HiSeq 2500 runs, the planning of which is shown. The exact make-up of queued runs is liable to change depending on the timing of completion of libraries. INVESTIGATOR: the UMGC unique project ID, in format Investigator_### # OF LANES: the number of high-output lanes requested LIBRARY STATUS (EST’D DATE): the date when libraries are expected in the sequencing suite. These include both UMGC-created and client-created libraries, and the estimated date may change due to a number of factors. If the library is QC'd and ready to load, this cell will be marked 'Done'. QUEUED RUN NAME: the name of the run in which the libraries are or will be sequenced -- these names refer to current or queued runs shown on the 2500 High-output Runs page # LANES FILLED: the number of lanes (out of 8) that have been filled for queued runs. Green shading indicated a filled flow cell, whereas red shading indicated that there are too few libraries accumulated to permit the run to proceed. Yellow shading indicates a flow cell that is 6/8 or 7/8 full, and that we may decide to sequence if the libraries have been waiting a long time in queue. ESTIMATED RUN DATE: the date at which queued runs are estimated to be launched.
7	Langlois_006	1	8/21/2017				Albrecht_004	2	7/26/17	B1
8	Jameson_011	1	8/10/2017	A3			Rothwell_001	2	8/4/2017	B1
9	Langlois_007	1	8/21/2017				Kobayashi2_002	3	8/7/17
10	Masopust_011	1	8/9/2017				Ward2_004	4	8/22/17
11	Bernlohr_053	3	8/21/2017				Duan_005	8	8/11/17	B3
12							Largaespada_116	1	8/21/17
13							Dunny_036	1	8/21/17
14							Marchant_004	0.5	8/25/17
15							Starr_039	0.5	8/21/2017
16							Vernick2_022	3	8/29/17
17							Yong_034	3	8/31/17
18							Jenkins_010	1	9/22/17
19							Schmidt_033	1	8/17/17
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27	1x100 bp Single Read Libraries						2x125 Paired-end ibraries
28	Investigator	# of Lanes	Library Status (Est'd Date)	Queued Run Name	# Lanes Filled	Estimated Run Date	Investigator	# of Lanes	Library Status (Est'd Date)	Queued Run Name	# Lanes Filled	Estimated Run Date
29							Harris_Project_076	2.5	7/7/17	A2
30							Finno2_013	3	7/10/17	Current B		Done
31							Bond_019	1	7/21/17	B2		Done
32							Finno_011	4	7/21/17			Done
33							Kashyap_006		7/24/17			Done
34							Sadowsky_151	1	7/26/17	Current A
35							Harris_081	4.5	7/26/2017	Current A
36							Springer_055	2	8/1/17	Current A
37							Dunny_035	1	8/8/17
38							Arbefeville_001/002	1	8/10/17	A2
39							Stupar_044	4	8/17/17
40							Peatman_002	1	8/17/17	A2
41							Marks_032	3	8/21/2017
42							Orr_029	3	8/25/2017
43							Novak_006	1	8/21/2017
44							McCue_031	1	8/22/17
45							Barney_017/Barney_019	1	9/11/17
46							Holding_006	1	9/1/17
47							SBG_Pilots	0.5	8.30.17
48							Baughn_015_repool	0.5	Done
49							Largaespada_119	2	9/11/17
50							Harris_083	4	9/12/2017
51							Bohjanen_030	5	8/22/17
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2	MiSeq Sample Queue. As libraries near completion, they are scheduled on MiSeq flow cells. There are five queues: 1) Standard Libraries, 2) VDL Libraries, 3) Harris Lab Libraries, 4) Expedited Libraries, and 5) Stowaway-Seq Libraries. (For Stowaway-Seq Queue, see the Stowaway-Seq Run Calendar tab.)
3	Standard Libraries (First-come, First-served, MiSeqs #1-#2) Standard runs are ordinarily scheduled on MiSeq #1 or #2, but may be run on MiSeqs #3- #5 if those instruments are open.							Veterinary Diagnostic Lab (VDL) Libraries (MiSeq #3) VDL samples receive priority on MiSeq #3, which is owned by the VDL and operated by the UMGC. Doug Marthaler of the VDL (marth027@umn.edu) is the gatekeeper for all VDL libraries. MiSeq #3 is used for "Standard" runs only when the VDL does not have libraries ready for sequencing.								Expedited Libraries (MiSeq #4) For clients who need more rapid turnaround, MiSeq #4 -- un unsubsidized instrument -- is reserved for their use. Although runs on MiSeq #4 are about 50% more expensive than on MiSeq #1 or #2, there is typically no queue to get on the instrument. MiSeq #4 is used for "Standard" runs only when there are no expedited libraries ready for sequencing.							Harris Lab Libraries (MiSeq #5) Harris Lab samples receive priority on MiSeq #5, which is owned by Dr. Harris and operated by the UMGC. MiSeq #5 is used for "Standard" runs only when the Harris lab does not have libraries ready for sequencing.
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5	Project	Run Type	# of Lanes	Samples Passed QC'd On	Estimated Library Completion	Run Status	MiSeq #	Project	Run Type	# of Lanes	Samples Passed QC'd On	Estimated Library Completion	VDL Priority	Run Status	MiSeq #	Project	Run Type	# of Lanes	Samples Passed QC'd On	Estimated Library Completion	Run Status	MiSeq #	Project	Run Type	# of Lanes	Samples Passed QC'd On	Estimated Library Completion	Run Status	MiSeq #
6	Alfano_003_Run_1	2x300 Version 3 Chemistry (16-22M Reads)	1	08-01-17	08-09-17			Mor_012	2x300 Version 3 Chemistry (16-22M Reads)	1	8/14/17	08/21/17	1	2. Queued Run #1	MiSeq #3
7	Johnson_080	2x300 Version 3 Chemistry (16-22M Reads)	2	08-01-17	08-09-17			Mor_010	2x300 Version 3 Chemistry (16-22M Reads)	1	7/25/17	8/15/2017	2	3. Queued Run #2	MiSeq #3
8	Kennedy_012	2x250 Version 2 Chemistry (8-12M Reads)	1	08-11-17	08-11-17			Phelps_017	2x300 Version 3 Chemistry (16-22M Reads)	1
9	Duan_005	2x150 Nano Run (1M Reads)	1		08-11-17			Phelps_018	2x300 Version 3 Chemistry (16-22M Reads)	1
10	Schmidt_034	2x150 Nano Run (1M Reads)	1		On Hold
11	Bindels_003	2x300 Version 3 Chemistry (16-22M Reads)	1	08-11-17	08-18-17
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38		# Future Lanes	7						# Future Lanes	4							# Future Lanes	0						# Future Lanes	0
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2	Stowaway-Seq Run Calendar.
3	Stowaway-Seq (2x300 PE MiSeq Runs) Stowaway-Seq is a service designed to provide shallow (≤ 2M reads), low-cost ($299.09) sequencing for small-scale pilot experiments. We achieve this by a) pooling projects from many different users, b) managing the addition of indexing barcodes to ensure that pooled libraries are compatible, and c) running all projects using a read length (2x300-bp PE) that encompasses any desired sequencing flavor. Please read FAQs below for more information, contact Allison Maclean (micbiom@umn.edu, 16S samples or amplicons) or Aaron Becker (becke044@umn.edu, other library types).
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5	Run Date and Status			Submission Cutoff Dates For Client-made Libraries		Submission Cutoff Dates For Amplicons or 16S Samples (Important: See FAQ #1!)		Lane Details
6	Scheduled Run Date	Days Until Run	Status	Cutoff Date	Days Remaining Until Cutoff Date	Cutoff Date	Days Remaining Until Cutoff Date	Project	# of 1/8th Lanes Requested	# of 1/8th Lanes Granted	Library Status	MiSeq #
7	Friday, 08-11-17	Will launch in -11 days.	Completed	Friday, 07-28-17	Cutoff date is past. This Stowaway-Seq run is closed.	Friday, 07-14-17	Cutoff date is past. This Stowaway-Seq run is closed for amplicon/16S sample submission.	Salomon_003	1
8								Faulk_001	1
9								Marcotte_003	1
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11								Hackel_008	1
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14								UMGC_350_GG_Even_BsmI	1
15	Friday, 08-18-17	Will launch in -4 days.	Completed	Friday, 08-04-17	Cutoff date is past. This Stowaway-Seq run is closed.	Friday, 07-21-17	Cutoff date is past. This Stowaway-Seq run is closed for amplicon/16S sample submission.	Baumler_001	4		Pass
16								Dunny_037	1		Pass
17								Moriarty_006	1		Pass
18								Yamamoto_012	1		Pass
19								-	-
20								-	-
21								-	-
22								Baumler_003	1
23	Friday, 09-15-17	Will launch in 24 days.	Next Up	Friday, 09-01-17	You have 10 days remaining to submit client-made libraries.	Friday, 08-18-17	Cutoff date is past. This Stowaway-Seq run is closed for amplicon/16S sample submission.	UMGC_350_GG_Even_BtsI	1
24								UMGC_389	1
25								Pankow_004	1
26								Schmidt_034	1
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31	Friday, 10-06-17	Will launch in 45 days.		Friday, 09-22-17	You have 31 days remaining to submit client-made libraries.	Friday, 09-08-17	You have 17 days remaining to submit amplicons or 16S samples.	UMGC_423	1
32								Kirkpatrick_003	4
33								-	-
34								-	-
35								-	-
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40	The following are our Stowaway-Seq Frequently Asked Questions (FAQs):
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42	1) Can I submit my own PCR amplicons and 16S full-service samples (samples for which the UMGC is carrying out 16S amplification) for Stowaway-Seq.
43	Yes, but with important caveats. Stowaway-Seq is primarily intended as a low-cost means to pilot new and challenging library creation methods. In other words, it is meant as a way to perform a basic sanity check on an NGS library before committing money to deep sequencing. Secondarily, it is a means to achieve inexpensive sequencing for amplicon libraries. Lastly, it is available for individuals who have a small number of 16S samples to submit to the UMGC's 16S workflow (too few to justify a full MiSeq lane). Hence, although you can submit your own amplicons or 16S samples for a Stowaway-Seq run, you may be bumped to a later Stowaway-Seq run if client-made libraries (higher priority) are submitted for the same run. This may occur even if these libraries are submitted after your amplicons or 16S samples. Also, due to the time required in the UMGC to prepare amplicons or 16S samples for sequencing, the cutoff date for such submissions is earlier than that for a client-made library.
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45	2) How much sequence will I get?
46	Users can request sequencing space in increments of 1/8th of a MiSeq lane – which yields approximately 1-2 million reads.
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48	3) How much space can I request?
49	You may request increments of 1/8th of a MiSeq Lane to a maximum of ½ lane, if space allows.
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51	4) What are the charges?
52	UMGC will charge users in increments of 1/8th of a lane ($299.09 per 1/8 th of a lane) requested.
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54	5) What samples are acceptable?
55	Libraries that have been indexed and pooled will be accepted one week before the Stowaway-Seq run date. We may accept samples for library creation for Stowaway service (e.g., amplicons or 16S samples), but ONLY when prior approval has been obtained, with enough time for the library creation to occur.
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57	6) Do you perform QC on libraries?
58	Yes. We perform Kapa QC on samples to ensure functional library.
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60	7) What is the deadline for submission?
61	For client-made libraries, the cut-off for submission is at least 7 days prior to the scheduled run. For amplicons and 16S samples, the cut-off for submission is at least 28 days prior to the scheduled run.
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63	8) Can I request Expedited Service for a Stowaway run?
64	No. The purpose of Stowaway-Seq is not speed, but low cost. The runs are scheduled in advance and guaranteed to run on the scheduled date, in order to provide a reliable, low-cost option for all.
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66	9) How do I request this service?
67	Please refer to this Google Doc to see the availibility of the next run.
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69	10) How can I know what barcodes to use for my samples – so that they do not overlap with another researcher’s barcodes?
70	Please email next-gen@umn.edu with your intended barcodes. We will check it against others currently in the run and notify you.
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72	11) What if I miss the deadline for submission?
73	UMGC will try to accommodate your request on the next scheduled run provided there is no barcode conflict.
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75	12) This is great, but I can't seem to get on a Stowaway-Seq run because they fill up too fast, and my submission type is of low priority according to your policies!!!
76	We have the ability to increase the frequency of Stowaway-Seq runs, and will do so if we find that demand justifies it.
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78	13) I still have questions. Who can I contact?
79	Please contact the Aaron Becker (Illumina Sequencing Services Manager) at becke044@umn.edu for questions regarding client-made library submission, or Allison Maclean (High-throughput Sequencing Services Manager) at micbiom@umn.edu for questions regarding amplicon or 16S sample submission.


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2	HiSeq 2500 Rapid Run samples submitted for library creation. As libraries near completion, they are scheduled on Rapid Run flow cells.
3	1x50 bp Single-read				2x50 Paired-end				2x100 Paired-end				2x250 Paired-end
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5	Investigator	# of Lanes	Samples QC'd On	Estimated Completion	Investigator	# of Lanes	Samples QC'd On	Estimated Completion	Investigator	# of Lanes	Samples QC'd On	Estimated Completion	Investigator	# of Lanes	Samples QC'd On	Estimated Completion
6									Bushley_020	1	4/5/2017	5/25/2017	Marthaler_050	1	8/11/2017	9/1/17
7									Bushley_024	1	7/24/2017	8/14/2017
8									Barney_016	1		8/25/2017
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14									1 X 100 bp Single Read				2 X 150 bp Paired-End
15									McCartney_006	3		07/28/17
16									Samac_007	4		8/24/17
17									Nimmakayala_002	2		08/21/17
18									Kolmer_001	3
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26	# Future Lanes	0			# Future Lanes	0				15			# Future Lanes	1
27	# Future Flow Cells	0			# Future Flow Cells	0			# Future Flow Cells	7.5			# Future Flow Cells	0.125


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2	Rapid Run HiSeq 2500 "Watson"				Rapid Run HiSeq 2500 "Crick"
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4	Flow cell: A		Flow cell: B		Flow cell: A		Flow cell: B
5	Running		Running		Idle		Idle
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7	Current Run		Current Run		Current Run		Current Run
8	Start	8/18/2017	Start	8/18/2017	Start		Start
9	End	8/20/2017	End	8/20/2017	End		End
10	Run Type	2x100-bp Paired End DI	Run Type	2x100-bp Paired End DI	Run Type		Run Type
11	Run ID		Run ID		Run ID		Run ID
12	Lane 1	TLSE_232	Lane 1	TLSE_233	Lane 1		Lane 1
13	Lane 2	TLSE_232	Lane 2	TLSE_233	Lane 2		Lane 2
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15	Queued Run #1		Queued Run #1		Queued Run #1		Queued Run #1
16	Start		Start		Start	8/23/2017	Start
17	End		End		End	8/25/2017	End
18	Run Type		Run Type		Run Type	1x100-bp Single Read DI	Run Type
19	Run ID		Run ID		Run ID		Run ID
20	Lane 1		Lane 1		Lane 1	Nimmakayala_002	Lane 1
21	Lane 2		Lane 2		Lane 2	Nimmakayala_002	Lane 2
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23	Queued Run #2		Queued Run #2		Queued Run #2		Queued Run #2
24	Start				Start		Start
25	End				End		End
26	Run Type				Run Type		Run Type
27	Run ID				Run ID		Run ID
28	Lane 1				Lane 1		Lane 1
29	Lane 2				Lane 2		Lane 2


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2		MiSeq #1 (Standard Sample Queue)		MiSeq #2 (Standard Sample Queue)		MiSeq #3 (VDL MiSeq) (Priority: VDL)		MiSeq #4 (Priority: Expedited Runs)		MiSeq #5 (Harris Lab MiSeq) (Priority: Harris Lab)
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4		Idle		Idle		Running		Idle		Idle
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6	Current Run	Start		Start		Start	8/10/2017	Start		Start
7		End		End		End	8/12/2017	End		End
8		Read Length		Read Length		Read Length	2x250 Version 2 Chemistry (8-12M Reads)	Read Length		Read Length
9		Queue Type		Queue Type		Queue Type	VDL Sample Queue	Queue Type		Queue Type
10		Projects		Projects		Projects	Mor_011	Projects		Projects
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12	Queued Run #1	Start	8/21/2017	Start	8/21/2017	Start		Start	8/21/2017	Start	8/21/2017
13		End	8/22/2017	End	8/24/2017	End		End	8/24/2017	End	8/24/2017
14		Read Length	2x150 Nano Run (1M Reads)	Read Length	2x300 Version 3 Chemistry (16-22M Reads)	Read Length	2x300 Version 3 Chemistry (16-22M Reads)	Read Length	2x300 Version 3 Chemistry (16-22M Reads)	Read Length	2x300 Version 3 Chemistry (16-22M Reads)
15		Queue Type	Standard Sample Queue	Queue Type	Standard Sample Queue	Queue Type	VDL Sample Queue	Queue Type	Standard Sample Queue	Queue Type	Standard Sample Queue
16		Projects	Duan_005	Projects	Alfano_003_Run_1	Projects	Mor_010	Projects	Johnson_080 Pool 2	Projects	Bindels_003
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18	Queued Run #2	Start	8/23/2017	Start		Start		Start		Start
19		End	8/24/2017	End		End		End		End
20		Read Length	2x150 Nano Run (1M Reads)	Read Length		Read Length		Read Length		Read Length
21		Queue Type	Standard Sample Queue	Queue Type		Queue Type		Queue Type		Queue Type
22		Projects	Echo_Repool	Projects		Projects		Projects		Projects
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24	Queued Run #3	Start		Start		Start		Start		Start
25		End		End		End		End		End
26		Read Length		Read Length		Read Length		Read Length		Read Length
27		Queue Type		Queue Type		Queue Type		Queue Type		Queue Type
28		Projects		Projects		Projects		Projects		Projects
29