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
The BioMicro Center operates the MiSeq i100 and provides access to NovaSeqX Plus through collaboration with nearby academic core facilities. Both instruments use Illumina's two-color XLEAP-SBS chemistry (G bases are inferred from signal absence) and are best suited to high-complexity libraries. UDIs are strongly recommended on both platforms.
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.
- Minimum 2 nM; 110 µL per lane.
- Custom sequencing primers: at least 30 µL at 100 µM of each primer type per flowcell. Contact biomicro@mit.edu before planning a custom library prep.
MiSeq i100
|
The MiSeq i100 uses XLEAP-SBS chemistry on a patterned (CMOS nanowell) flowcell and is the BMC's walkup-capable instrument. It supports the longest read lengths of any instrument in the center (up to 1000 nt), making it ideal for amplicon panels, 16S rRNA surveys, validation runs, and other applications where read length matters more than throughput. Kits available: 100 nt (25M, 100M), 300 nt (5M, 25M, 100M), 600 nt (5M, 25M, 50M), 1000 nt (25M). Run times range from under 4 hours (25M 100 nt) to ~24 hours (100M 300 nt). Walkup service is not available to external users. Runs must be scheduled in the iLabs calendar. Server training and storage access on BMC servers is required. Custom sequencing primers: At least 15 µL of each primer type at 100 µM must be provided per flowcell. Contact biomicro@mit.edu before planning a custom library prep. 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. We maintain minimal reagent stocks so turn around times may vary.
| Kit | Approx. reads | Notes |
|---|---|---|
| 70 nt (V2) | ~15M | 30 or 70 SE |
| 150 nt (V3) | ~25M | 75 PE |
| 300 nt (V2) | ~15M | 150 PE |
| 500 nt (V2) | ~15M | 250 PE |
| 600 nt (V3) | ~25M | 300 PE |
| 500 nt NANO | ~1M | Reduced output run |
See MIT:Pricing · BioMicroCenter:Pricing for kit pricing. Custom sequencing primers follow the same submission guidelines as the MiSeq i100: at least 15 µL at 100 µM per primer type.
Element Biosciences
The BioMicro Center operates an AVITI24 from Element Biosciences. The AVITI24 uses Element's proprietary Avidity Base Chemistry (ABC), a 4-color sequencing approach that achieves high base-call accuracy (>80% of reads Q40+) by leveraging multivalent binding of avidites rather than single-nucleotide incorporation. The random flowcell and rolling-circle amplification approach produce low levels of index hopping and optical duplicates compared to patterned-flowcell instruments. Beyond standard NGS, the AVITI24 supports Teton CytoProfiling for direct in-cell co-detection of RNA, protein, and morphology — see Spatial Services for details.
AVITI24
|
Kits and run times:
Each flowcell has two independently-addressable lanes. Both lanes must be loaded to run a flowcell, but each can carry a different library pool. 300PE kits are single-lane only. Anchors: The BMC runs P5/P7-anchored (Illumina Freestyle) libraries as standard. Element Adept (SP5/SP27) libraries are also supported but require a 5′-phosphate on the forward strand for circularization — contact biomicro@mit.edu before preparing Adept libraries. Indexing: Index orientation differs from standard Illumina: indexes are read from antisense primers with the P7-side first (index 1). Provide index sequences as read on the instrument, not as ordered. For dual-indexed libraries this is typically antisense to the ordered oligo sequence. Custom primers: 70 µL at 100 µM for Read 1; 40 µL at 100 µM for all other reads. Custom primers must not interfere with other users' samples in the same lane. Minimum read guarantee: Guaranteed 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
The BioMicro Center operates a G4 from Singular Genomics. The G4 uses a 4-color SBS chemistry on a patterned flowcell and delivers index-hopping rates comparable to non-patterned Illumina instruments (HiSeq/GAIIx level) — substantially lower than X-Amp patterned flowcells. This makes it a practical choice for experiments that do not require UDIs. The G4 supports four independently-addressable lanes per flowcell and up to four flowcells per run, offering per-lane flexibility at competitive per-lane cost.
G4
|
Kits and run times:
Library submission: Submit standard Illumina (P5/P7) libraries. The BMC converts the pool to S1/S2 anchors by PCR prior to sequencing — do not submit S1/S2-anchored libraries directly. Indexing: After conversion, indexes are read from S1 (index 1) then S2 (index 2), in the same orientation as ordered in classical Illumina library preps. Dual 8-nt indexes are required for all lane-by-lane sequencing. Custom index primers are not permitted. Lane by lane:
Minimum read guarantee: Guaranteed 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) | Random |
| 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
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 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.