UMGC Sequencer Home


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2	High-output HiSeq 2500 ("Franklin") Run Calendar				Last updated on 06/23/2017. 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	Running		Running
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7	Current Run in Position A		Current Run in Position B
8	Start	6/22/2017	Start	6/22/2017
9	End	6/25/2017	End	6/26/2017
10	Elapsed	Has been running for 3 days.	Elapsed	Has been running for 3 days.
11	Run Type	2x50-bp Paired End DI	Run Type	2x50-bp Paired End DI
12	Run ID	HS4_FC_A_06_21_17	Run ID	HS4_FC_B_06_22_17
13	Lane 1	Garry_048	Lane 1	Drewes_004 (0.5)
14	Lane 2	Robertson_017	Lane 2	Hicks_014 (0.5) Hu_024 (0.5)
15	Lane 3	Robertson_017	Lane 3	Jenkins_008
16	Lane 4	Robertson_017	Lane 4	Vezys_004
17	Lane 5	Robertson_017	Lane 5	Vezys_004
18	Lane 6	Bardwell_035	Lane 6	Vezys_004
19	Lane 7	Blazar_002	Lane 7	Vezys_004
20	Lane 8	Blazar_002 (0.5)	Lane 8	Gralnick_019 Reseq
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22	Queued Run A1		Queued Run B1
23	Est'd Start	TBD	Est'd Start
24	Est'd End		Est'd End
25	Run Type	1x50-bp Single Read DI	Run Type
26	Lane 1	Slattery_008	Lane 1
27	Lane 2	Modiano_030	Lane 2
28	Lane 3	Masopust_010	Lane 3
29	Lane 4	Gardner_002	Lane 4
30	Lane 5		Lane 5
31	Lane 6		Lane 6
32	Lane 7		Lane 7
33	Lane 8		Lane 8
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35	Queued Run A2		Queued Run B2
36	Est'd Start	TBD	Est'd Start	6/26/2017
37	Est'd End		Est'd End	7/3/2017
38	Run Type	1x50-bp Single Read DI	Run Type	2x125-bp Paired-End DI
39	Lane 1	Slattery_008	Lane 1	Dweikat_001
40	Lane 2	Modiano_030	Lane 2	Dweikat_001
41	Lane 3	Masopust_010	Lane 3	Baughn_015 Reseq
42	Lane 4	Gardner_002	Lane 4	Baughn_015 Reseq (0.5)
43	Lane 5		Lane 5	Weiblen_001_Pool1
44	Lane 6		Lane 6	Weiblen_001_Pool1
45	Lane 7		Lane 7	Weiblen_001_Pool1
46	Lane 8		Lane 8	Weiblen_001_Pool1
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48	Queued Run A3		Queued Run B3
49	Est'd Start	TBD	Est'd Start	TDB
50	Est'd End		Est'd End
51	Run Type	26x98-bp Paired-End	Run Type	2x125-bp Paired-End DI
52	Lane 1	Jameson_Project_010_D12_P14	Lane 1	Weiblen_001_Pool1
53	Lane 2	Binstadt_Project_004	Lane 2	Weiblen_001_Pool1
54	Lane 3	Asakura_Project_017	Lane 3
55	Lane 4	Starr_034-037	Lane 4
56	Lane 5	Starr_034-037	Lane 5
57	Lane 6	Starr_034-037	Lane 6
58	Lane 7	Starr_034-037	Lane 7
59	Lane 8	Starr_034-037	Lane 8


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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							Drewes_004	0.5	5/25/17	B1	7/8		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	Slattery_008	1	5/24/2017	A2			Hicks_014	0.5	5/24/17	B1
8	Modiano_030	1	6/13/2017	A2			Vezys_004	4	6/20/17	B1
9	Masopust_010	1	6/12/2017	A2			Jenkins_008	1	5/25/17	B1
10	Gardner_002	1	6/14/2017	A2			Gralnick_019 Reseq	1	Done	B1
11							Afrin_003	8	5/25/17	Current B	8/8
12							Robertson_017	4	6/21/17	A1
13							Blazar_002 (?)	1.5	6/12/17	A1
14							Bardwell_035	1	6/12/17	A1
15							Garry_048	1	6/7/17	A1
16							Hu_024	0.5	6/7/17	B1
17							Kyba_067	1	7/19/17
18							Slattery_007	1	6/7/17
19							Garry_051	3	6/23/17
20							Cichocki_006	1.5	7/6/17
21							Robinson_003	0.5	7/7/2017
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25
26
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
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33							Orr_028	3.5	5/25/2017	A1	7/8	6/9/2017
34							Knights3_007 Pool 4	1	Done
35							Chen2_001	1	5/25/17
36							Dehm_033	1	6/5/2017
37							Knights3_007 Pool 3	1	Done
38							Weiblen_001_Pool1	6	Done		6/8
39							Dweikat_001	2	Done	B2
40							Weiblen_001_Pool2	1	6/23/17
41							Muehlbauer_026	6.5	6/20/17
42							SBG pilots	0.5	Pending
43							McCue_031	1	6/16/2017
44							Riehle_001	2	6/14/2017
45							Baughn_015 Reseq	1.5	Done	B2
46							Zempleni_004	0.5	7/6/2017
47							Harris_Project_076	2.5	7/7/17
48							Springer_054	2	6/21/17
49							Garry_049	0.5	6/23/17
50							Carter_012	3.5	7/17/2017
51							Israni_008	0.5	7/17/2017
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53							Dehm_031	0.33	Hold to seq with Dehm_032
54							Dehm_035	0.33	Hold to seq with Dehm_032


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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	Bushley_019_Pool 2 Reseq	2x300 Version 3 Chemistry (16-22M Reads)	2		05-26-17	TBD		Mor_Project_006	2x250 Version 2 Chemistry (8-12M Reads)	1	06-14-17	---				Sadowsky_150	2x300 Version 3 Chemistry (16-22M Reads)	1		06-15-17
7	MDL Run	2x250 Version 2 Chemistry (8-12M Reads)	1		05-31-17	TBD		Mor_Project_007	2x250 Version 2 Chemistry (8-12M Reads)	1	---	---
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9	Blekhman_022	2x250 Version 2 Chemistry (8-12M Reads)	1	06-05-17	06-12-17	2. Queued Run #1	MiSeq #2
10	Bushley_022	2x300 Version 3 Chemistry (16-22M Reads)	1	06-07-17	06-15-17	1. Running	MiSeq #5
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12	Hackel_006	2x300 Version 3 Chemistry (16-22M Reads)	1	06-13-17	06-16-17	TBD
13	Perlingero_036	2x75 Version 3 Chemistry (16-22M Reads)	1	06-20-17	06-20-17	3. Queued Run #2
14	Hendrickson_009	2x150 Nano Run (1M Reads)	1	06-20-17	06-23-17	TBD
15	Jenkins_011	2x150 Nano Run (1M Reads)	1	06-20-17	06-23-17	TBD
16	Bushley_022 Reseq	2x300 Version 3 Chemistry (16-22M Reads)	1
17	Hoffmann_002	2x300 Version 3 Chemistry (16-22M Reads)	1	06-09-17	06-22-17
18	Kinkel_041_Pool 1	2x300 Version 3 Chemistry (16-22M Reads)	1	06-13-17	06-22-17
19	Kinkel_041_Pool 2	2x300 Version 3 Chemistry (16-22M Reads)	1	06-13-17	06-22-17
20	Kinkel_041_Pool 3	2x300 Version 3 Chemistry (16-22M Reads)	1	06-13-17	06-22-17
21	MySeq_Stwowaway_025	2x300 Version 3 Chemistry (16-22M Reads)	1		06-30-17
22	Johny_001	2x300 Version 3 Chemistry (16-22M Reads)	1	06-23-17	06-27-17	TBD
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39		# Future Lanes	16						# Future Lanes	2							# Future Lanes	1						# 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, 06-09-17	Will launch in -16 days.	Completed	Friday, 05-26-17	Cutoff date is past. This Stowaway-Seq run is closed.	Friday, 05-12-17	Cutoff date is past. This Stowaway-Seq run is closed for amplicon/16S sample submission.	Sadowsky_146	2	2	Pass
8								UMG_418	0.1
9								Elias_005	1	1	Pass
10								Hunter_013	1	1	Pass
11								Vernick_015	1	1
12								Friedenburg_003	1	1	Pass
13								Hackel_005	1	1
14								Yamamoto_010	1	1	Pass
15	Friday, 06-30-17	Will launch in 5 days.		Friday, 06-16-17	Cutoff date is past. This Stowaway-Seq run is closed.	Friday, 06-02-17	Cutoff date is past. This Stowaway-Seq run is closed for amplicon/16S sample submission.	Yamamoto_011	2
16								-	-
17								Harris3_002_003_Check	1		Pass
18								Baughn_016	1		done
19								Kaznessis_010	1
20								Bishop2_002	1		Pass
21								Melchior_001	2
22								-	-
23	Friday, 07-21-17	Will launch in 26 days.		Friday, 07-07-17	You have 12 days remaining to submit client-made libraries.	Friday, 06-23-17	Cutoff date is past. This Stowaway-Seq run is closed for amplicon/16S sample submission.	Sadowsky_149	1
24								Friedenberg_004	2
25								-	-
26								UMGC_420_16S	1
27								UMGC_420_shotgun	1
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31	Friday, 08-11-17	Will launch in 47 days.		Friday, 07-28-17	You have 33 days remaining to submit client-made libraries.	Friday, 07-14-17	You have 19 days remaining to submit amplicons or 16S samples.
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39
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		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)
3		2x75 = $1,228.68 2x250 PE = $1,518.39 2x300 PE = $1,968.50	2x75 = $1,228.68 2x250 PE = $1,518.39 2x300 PE = $1,968.50	2x75 = $1,228.68 2x250 PE = $1,518.39 2x300 PE = $1,968.50	2x75 = $1,228.68 2x250 PE = $1,518.39 2x300 PE = $1,968.50 2x300 PE (Expedited) = $3,210.19		2x75 = $1,228.68 2x250 PE = $1,518.39 2x300 PE = $1,968.50
4		Idle	Idle	Idle	Idle		Idle
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6	Current Run	Start	Start	Start	Start		Start
7		End	End	End	End		End
8		Read Length	Read Length	Read Length	Read Length		Read Length
9		Queue Type	Queue Type	Queue Type	Queue Type		Queue Type
10		Projects	Projects	Projects	Projects		Projects
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12	Queued Run #1	Start	Start	Start	Start	6/23/2017	Start	6/23/2017
13		End	End	End	End	6/26/2017	End	6/26/2017
14		Read Length	Read Length	Read Length	Read Length	2x300 Version 3 Chemistry (16-22M Reads)	Read Length	2x300 Version 3 Chemistry (16-22M Reads)
15		Queue Type	Queue Type	Queue Type	Queue Type	Standard Sample Queue	Queue Type	Standard Sample Queue
16		Projects	Projects	Projects	Projects	Bushley_019_Pool 2 Run 2 (add Mock)	Projects	Bushley_022 (add Mock)
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18	Queued Run #2	Start	Start	Start	Start		Start
19		End	End	End	End		End
20		Read Length	Read Length	Read Length	Read Length		Read Length
21		Queue Type	Queue Type	Queue Type	Queue Type		Queue Type
22		Projects	Projects	Projects	Projects		Projects
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24	Queued Run #3	Start	Start	Start	Start	6/19/2017	Start
25		End	End	End	End	6/21/2017	End
26		Read Length	Read Length	Read Length	Read Length	2x300 Version 3 Chemistry (16-22M Reads)	Read Length
27		Queue Type	Queue Type	Queue Type	Queue Type	Expedited Sample Queue	Queue Type
28		Projects	Projects	Projects	Projects	Sadowsky_150 Reseq?	Projects
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1
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	Idle		Idle		Idle		Idle
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7	Current Run		Current Run		Current Run		Current Run
8	Start		Start		Start	6/23/2017	Start	6/23/2017
9	End		End		End	6/25/2017	End	6/25/2017
10	Run Type		Run Type		Run Type	2x100-bp Paired End DI	Run Type	2x100-bp Paired End DI
11	Run ID		Run ID		Run ID		Run ID
12	Lane 1		Lane 1		Lane 1	TLSE_220	Lane 1	TLSE_221
13	Lane 2		Lane 2		Lane 2	TLSE_220	Lane 2	TLSE_221
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15	Queued Run #1		Queued Run #1		Queued Run #1		Queued Run #1
16	Start	6/20/2017	Start	6/20/2017	Start		Start
17	End	6/23/2017	End	6/23/2017	End		End
18	Run Type	2x250-bp Paired-End DI	Run Type	2x250-bp Paired-End DI	Run Type		Run Type
19	Run ID		Run ID		Run ID		Run ID
20	Lane 1	LaPara_032	Lane 1	LaPara_032	Lane 1		Lane 1
21	Lane 2	LaPara_032	Lane 2	LaPara_032	Lane 2		Lane 2
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23	Queued Run #2		Queued Run #2		Queued Run #2		Queued Run #2
24	Start				Start	TBD	Start
25	End				End		End
26	Run Type				Run Type	2x100-bp Paired-End	Run Type
27	Run ID				Run ID		Run ID
28	Lane 1				Lane 1	Bushley_020	Lane 1
29	Lane 2				Lane 2	Bushley_024	Lane 2


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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	LaPara_032	4	6/2/2017	6/16/17
7									Bushley_024	1
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14									1 X 100 bp Single Read				2 X 150 bp Paired-End
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26	# Future Lanes	0			# Future Lanes	0				2			# Future Lanes	4
27	# Future Flow Cells	0			# Future Flow Cells	0			# Future Flow Cells	1			# Future Flow Cells	0.5