BioSquared

A bioinformatics platform for workflow automation.

GxP evidence layer

Ingests provenance Nextflow already emits, producing signed, tamper-evident validation records. Works wherever pipelines run.

CRO deliverable layer

White-label reports letting biologists read their own spatial data. Interactive, branded, publication-ready figures.

Cloud waste analyzer

Read-only AWS analysis surfacing genomics-specific waste generic tools miss. Ranked findings, real dollars.

Antibody Sequencing Automation

Automates antibody sequencing workflows end to end, from raw reads to annotated output, without manual scripting.

GxP Evidence layer

Audit-ready evidence, verifiable in one click.

DOC ID · DASHBOARD · ORG · ATLAS BIO · STATUS · LIVE

Validation status

Pipelines registered	4
Versions validated	6
Versions in qualification	2
Validation packages approved	3
Open deviations	1

Recent runsAll runs

Run	Pipeline / version	Status	Started
rnaseq-2026-07-14	rnaseq-nf · 2.4.1	Completed	07-14 09:22
sarek-nightly	sarek · 3.1.0	Running	07-14 08:50
methylseq-batch-7	methylseq · 1.0.0	Failed	07-13 22:10
rnaseq-2026-07-13	rnaseq-nf · 2.4.1	Completed	07-13 14:05

CRO Analyzer

Spatial biology, from tissue to markers.

SAMPLE · V19-2043-A1 · VISIUM · READY

Tissue map

Color the tissue by

Regions · click to isolate

Antibody Sequencing

Raw reads to clonotypes and lineages, end-to-end.

JOB · AB-2043 · PIPELINE V2 · IGBLAST

Sequencing workflow

1,240,338

Reads processed

96.4%

Passing QC

88.1%

Productive V(D)J

3,412

Unique clonotypes

Samples

FASTQ Input1.24M readsDone

IgBLAST Annotation88.1% productiveDone

Clonal Analysis3,412 clonotypesDone

Lineage Trees214 lineagesRunning

Insightsreport pendingQueued

The agent ran qc_filter_convert_igblast end-to-end: quality filtering, FASTQ→FASTA conversion, V(D)J annotation, then clonotype clustering by CDR3 similarity. Lineage reconstruction is in progress.

Cloud Waste Analyzer

Cut cloud spend — without deleting a single read.

$ cloudwaste analyze --cur cur.csv --inventory inv.csv --trace-dir traces/
    --account-label genomics-prod --out-html report.html --out-pdf report.pdf
Loading CUR 2.0 export ············ 312,480 line items
Scanning S3 inventory ············ 48,912 objects
Classifying genomic files ········ done · 6 traces
Storage waste
✔1,204 BAMs re-derivable from FASTQ, aging in hot storage$1,842.60/mosafe
✔Duplicate reference genome + BWA index × 7 prefixes$318.04/mosafe
✔2,317 Nextflow work/ intermediates (outputs published)$204.55/mosafe
Compute waste
✔gatk_haplotypecaller: 64 GiB asked, 11 GiB peak — rightsize$893.11/moreview
✔12 unattached EBS volumes, 90+ days idle$277.40/mosafe
○bwa_mem is spot-safe (short, restartable, sharded)$610.22/mocareful
FASTQ · VCF · unknown files → kept, never flagged for deletion
────────────────────────────────────────────────
$4,145.92 / monthaddressable waste · 6 findings
report → report.html · report.pdf

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