BioMicroCenter:ShortRead
HOME -- SEQUENCING -- LIBRARY PREP -- HIGH-THROUGHPUT -- COMPUTING -- OTHER TECHNOLOGY
The MIT BioMicro Center offers short-read sequencing on five platforms from three manufacturers, spanning low to high output. All sequencing includes library quality control (RT-PCR and Fragment Analyzer), demultiplexing, and FASTQ delivery. Pricing is available to MIT users at MIT:Pricing and to all users at BioMicroCenter:Pricing.
Choosing a platform? Jump to platform comparison and FAQ below, or contact biomicro@mit.edu.
OUTPUT TIERS
| OUTPUT | PLATFORM | READS / UNIT | MIN SUBMISSION | TYPICAL USE |
|---|---|---|---|---|
| HIGH |  NovaSeqX Plus |
1.2B reads/lane (10B FC) 3.0B reads/lane (25B FC) |
110 µL at 2 nM per lane | Largest experiments requiring billions of reads: cohort-scale WGS, ultra-deep sequencing, high-replicate RNA-seq studies |
| Available through collaboration with nearby academic shared resources. Contact BMC staff to inquire. | ||||
| MID |  Element AVITI24 |
~400M reads/lane (~800M per 2-lane flowcell) |
15 µL at 2 nM | Standard depth experiments: RNA-seq, ChIP-seq, ATAC-seq, WGS at moderate coverage; tolerates low-complexity libraries well |
| LOW |  Singular G4 |
~100M reads/lane (4 lanes/flowcell) |
12 µL at 4 nM | Smaller experiments, amplicons, validation, pilot studies, and applications where cost-per-lane is the primary driver |
 MiSeq i100 |
5M – 100M reads/flowcell | 40 µL at 2 nM | ||
MiSeq classic |
1M – 25M reads/flowcell | 40 µL at 2 nM | ||
| MiSeq classic is off contract and will be retired upon instrument failure. MiSeq i100 offers walkup service (MIT only, training required). | ||||
SEQUENCING PLATFORMS
Illumina
NovaSeqX Plus
NovaSeqX Plus sequencing is available through BMC's collaboration with local academic core facilities, and is well suited to projects requiring the deepest coverage or largest sample counts. It is only available for MIT users. These collaborations provide advantaged pricing to MIT users.
- See Pricing for rates.
- Full flowcells (8 lanes, 10B or 25B) have priority over individual lanes; wait times for single lanes can vary.
MiSeq i100
|
The MiSeq i100 uses Illumina's XLEAP-SBS chemistry on a patterned (CMOS nanowell) flowcell. It is the BMC's walkup-capable instrument, suited to amplicon panels, 16S rRNA surveys, validation runs, and applications requiring long reads (up to 1000 nt). Kits available: 100 nt (25M, 100M), 300 nt (5M, 25M, 100M), 600 nt (5M, 25M, 50M), 1000 nt (25M). Walkup service is not available to external users. Runs must be scheduled in the iLabs calendar. Thanks to: MIT VPR, Drs. Gene Li, Michael Birnbaum, Dept. of Biology, Scott Ritterbush '89 SM '92 |
MiSeq classic
The MiSeq classic uses 4-color SBS chemistry on a non-patterned (random cluster) flowcell. It is available for users with established protocols on v2/v3 chemistry, but is off contract and will be retired upon instrument failure.
| Kit | Approx. reads | Notes |
|---|---|---|
| 70 nt (V2) | ~5M | 30 or 70 SE |
| 150 nt (V3) | ~5M | 75 PE |
| 300 nt (V2) | ~5M | 150 PE |
| 500 nt (V2) | ~10M | 250 PE |
| 600 nt (V3) | ~15M | 300 PE |
| 500 nt NANO | ~1M | Reduced output run |
See MIT:Pricing · BioMicroCenter:Pricing for kit pricing.
Element Biosciences
AVITI24
|
ANCHORSElement supports both Illumina anchors (P5/P7) using Freestyle chemistry and Element anchors (SP5/SP27) for Adept chemistry. For standard runs at the BMC, P5/P7-anchored (Illumina) libraries are preferred. Element Adept libraries (SP5/SP27) require a 5′-phosphate on the forward end to circularize. INDEXINGCompared to Illumina, AVITI24 read direction is similar to Illumina's Forward Strand workflow for Dual Indexed Libraries. Indexes are read from antisense primers — P7 side first (index 1). Index sequences should be provided as read, not as ordered.
SINGLE LANEEach lane of the AVITI24 can be loaded independently; both lanes must be filled to run a flowcell. 300PE kits support only a single lane. Custom primers must not interfere with other users' samples. All non-standard requests require a full flowcell. MINIMUM READ GUARANTEEGuaranteed if: (a) BMC performed QC, (b) library diversity is high (especially in the first 5 bases of Read 1), and (c) concentration ≥ 2 nM. Thanks to: Element Biosciences; Scott Ritterbush |
Singular Genomics
G4
|
LIBRARY SUBMISSIONSubmit standard Illumina (P5/P7) libraries. The BMC will convert the pool to S1/S2 anchors by PCR prior to sequencing — do not submit S1/S2-anchored libraries directly. INDEXINGIndexes are read from the S1/S2 anchor sequences after conversion. Index 1 is read from S1, index 2 from S2. Index sequences are the same orientation as ordered in classical Illumina library preps. Dual indexes (8 nt) are required for all lane-by-lane sequencing. Custom index primers are not permitted. LANE BY LANE
MINIMUM READ GUARANTEEGuaranteed if: (a) BMC performed QC, (b) no custom primers, and (c) concentration ≥ 4 nM. Thanks to: Singular Genomics |
PLATFORM COMPARISON
| SPEC | NovaSeqX Plus | Element AVITI24 | Singular G4 | MiSeq i100 | MiSeq classic |
|---|---|---|---|---|---|
| Read lengths | 100 nt, 300 nt | 75 PE, 150 PE, 300 PE | 50 PE, 150 PE | 100–1000 nt | 70–600 nt |
| Flowcell type | Patterned (X-Amp) | Random | Patterned | Patterned (CMOS nanowell) | Non-patterned (random cluster) |
| Chemistry | 2-color XLEAP-SBS (G=dark) | 4-color avidity SBS | 4-color SBS | 2-color XLEAP-SBS (G=dark) | 4-color SBS |
| Index hopping | High — UDIs required | Low — UDIs not needed | Low (patterned, non-XLEAP) | Present — UDIs recommended | Low (non-patterned) |
| Low-complexity libraries | Struggles | Handles well | Handles well | Struggles | Handles well |
| Lane flexibility | Lane-by-lane (full FC priority) | Lane-by-lane | Lane-by-lane | Full flowcell only | Full flowcell only |
| Walkup | No (collaboration) | No | No | Yes (training required) | No |
| Illumina lib compatible | Yes (native) | Yes (P5/P7 Freestyle) | Yes — BMC converts pool by PCR | Yes (native) | Yes (native) |
| Donated / supported by | Local core collaboration | Element Biosciences; Scott Ritterbush | Singular Genomics | MIT VPR; Drs. Gene Li, Michael Birnbaum; Dept. of Biology; Scott Ritterbush '89 SM '92 |
FAQ
How do I choose the right platform?
Start with your read count requirement and library type:
- Millions of reads or fewer → MiSeq i100 (amplicons, long reads up to 1000 nt) or Singular G4 (most cost-effective for standard 50/150 PE).
- Hundreds of millions of reads → Element AVITI24 (lane-by-lane flexibility, low index hopping, tolerates low-complexity libraries).
- Billions of reads → NovaSeqX Plus (contact BMC to coordinate flowcell sharing).
Can I use my existing Illumina libraries?
- AVITI24 – Yes. P5/P7 libraries run natively using Freestyle chemistry.
- MiSeq i100 / classic – Yes. Standard Illumina libraries run natively.
- Singular G4 – Yes. Submit standard P5/P7 libraries; the BMC converts the pool to S1/S2 anchors by PCR. Do not submit S1/S2 libraries directly.
- NovaSeqX Plus – Yes. Standard Illumina libraries run natively.
What are the minimum submission requirements?
- AVITI24: 15 µL at 2 nM
- MiSeq i100 / classic: 40 µL at 2 nM
- Singular G4: 12 µL at 4 nM
- NovaSeqX Plus: 110 µL per lane at 2 nM (contact BMC)
My library has low complexity. Which platform should I use?
Avoid the NovaSeqX Plus and MiSeq i100 — both use 2-color XLEAP-SBS chemistry where G bases are inferred from signal absence, making low-diversity early cycles prone to run failure. The AVITI24, Singular G4, and MiSeq classic all use 4-color chemistry and handle low-complexity libraries well. Always contact biomicro@mit.edu before submitting unconventional libraries.
Do I need unique dual indexes (UDIs)?
- NovaSeqX Plus – Yes, required (patterned X-Amp flowcell).
- MiSeq i100 – Recommended (patterned CMOS flowcell).
- AVITI24 – Not required; index hopping is low on random flowcells.
- Singular G4 – Not required; patterned but does not use X-Amp chemistry; hopping is on par with HiSeq/GAIIx.
- MiSeq classic – Not required; non-patterned flowcell has low hopping.
How long until my data is delivered?
Queue times are typically short — most samples run within a few days. Full flowcells have sequencing priority over individual lanes. Contact biomicro@mit.edu for current wait times.
How long is my data stored?
- FASTQ files: 1 year for AVITI24, Singular G4, MiSeq i100.
- BCL files (MiSeq): 30 days.
- Long-term storage is available; see BioMicroCenter:Pricing for active storage and tape archive options.
What quality control is included?
All runs include a final pool QC (RT-PCR and Fragment Analyzer) and post-sequencing QC (FastQC, run metrics, alignment rate, complexity, RNAseq metrics where applicable, contamination checks). Users who opt out of pre-sequencing QC by providing their own concentration forfeit read guarantees.
Can I pool samples from multiple labs?
Yes, but users are responsible for minimizing index cross-contamination and index crosstalk. The BMC does not combine projects within a lane.
SUBMISSION
All sequencing is submitted through iLabs. External users should contact biomicro@mit.edu directly. Samples must meet the minimum volume and concentration requirements listed above; coordinate with BMC staff before sending non-standard submissions.
Additional services: