Comparing tools for sequencing facilities

Five families, three domains

The 19 tools here sort into a handful of families. Sequencing LIMS (Clarity, MISO, SLIMS) track samples, libraries and runs. Core-facility management systems (iLab, PPMS) run the booking-and-billing front desk for a shared resource. Pipeline and analysis platforms (Galaxy, Seqera, DNAnexus, Terra, Illumina ICA, Latch, MGnify) execute the bioinformatics. Submission tools (ENA Webin, COPO) deposit data into public archives. And electronic lab notebooks (Benchling, eLabFTW, and the notebook side of openBIS, LabKey and SLIMS) record the bench work.

Underneath the families, three functional domains describe what a tool actually touches: managing the facility and its samples (a LIMS plus an order desk), executing pipelines, and submitting to a public archive like ENA. Most tools live squarely in one domain; a few straddle two. Hover the domains below to see who falls where.

Of the 19 tools, 5 offer a researcher-to-facility order intake, 8 run pipelines, and 4 submit to ENA — but only 1 does all three. That tool is SeqDesk, which this site documents; it’s included here as one row among the rest, scored on the same rubric and with the same coarse marks.

The capability matrix

Here is the whole comparison in one grid. Each cell is a coarse mark — native, partial (a capability that exists but is indirect or weak), or absent — because the goal is the shape of each tool’s coverage, not a number. Filter by category, sort by any capability, and click a row for a one-line description with licensing and pricing.

A few patterns fall out. The LIMS tools own the left of the table — order intake, sample and run tracking — and thin out toward analysis and submission. The pipeline platforms are the mirror image: dense in the middle, empty at the front desk. ENA submission is rare and tends to be the whole product (Webin, COPO) rather than one feature of a larger system. And a notebook/ELN — common across Benchling, openBIS, LabKey, eLabFTW and the cloud pipeline platforms — is the one column where SeqDesk is blank, which makes those tools natural companions rather than substitutes.

Breadth vs. openness

Two axes capture much of the trade-off a facility weighs. The horizontal axis is breadth — does a tool do one thing, or chain the whole order-to-archive lifecycle? The vertical axis is openness — proprietary cloud service at the bottom, open-source and self-hostable at the top. The dense lower-left is the crowd of focused commercial products; the top-left holds the open single-purpose tools; the broad proprietary suites sit lower-right.

Choosing by job

No single tool is the answer for every facility; the right pick depends on which job is the bottleneck.

• Booking, scheduling and recharge billing across many instruments. iLab and Stratocore PPMS are purpose-built for this and go well beyond what sequencing-specific tools attempt.
• Receipt-to-result sample and run tracking at scale. The mature LIMS — Clarity, SLIMS, or open-source MISO — are built around exactly this spine.
• Industrial pipeline execution. Seqera, DNAnexus, Illumina ICA and Latch are designed to run Nextflow/nf-core (and WDL/CWL) at cloud or HPC scale, with observability the others don’t match.
• Getting data into a public archive correctly. ENA Webin is the canonical path; COPO adds checklist-validated brokering for large consortia.
• An electronic lab notebook. Benchling (commercial) and eLabFTW or openBIS (open-source) are the reference points — and pair cleanly with any of the above.
• One self-hosted system that chains intake, pipelines and ENA submission. This is the niche SeqDesk was built for, and — per the matrix — the one combination no other single tool currently covers. Facilities wanting heavier compute often pair it with a runner like Seqera, and an ELN like eLabFTW.