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23rd Pair Lab Limited

Software

Software we build
and run ourselves

Three independent analysis tools, each built for a question we get asked often. Every one takes raw sequencing data through to a result, without you assembling a pipeline out of parts.

Variant analysis, end to end

23rdExon

Raw reads through to called, annotated and interpreted variants in a single workflow. Alignment, variant calling, annotation and analysis are one run rather than four tools you have to join up yourself.

Input

FASTQ or aligned BAM

Main analysis

Alignment, small and structural variant calling, annotation, classification

Output

Annotated VCF, evidence-backed report, intermediate files

Use model

Licensed to run on your own infrastructure

  1. FASTQraw reads
  2. Alignto reference
  3. CallSNV / indel / SV
  4. AnnotateVEP, SnpEff
  5. ClassifyACMG/AMP
  6. Reportwith evidence
Variant types
SNVs, indels, copy-number variants and structural variants.
Reference builds
GRCh38/hg38 and GRCh37/hg19.
Alignment & calling
BWA-MEM alignment; GATK HaplotypeCaller and DeepVariant for small variants; Manta and CNVkit for structural and copy-number events.
Annotation
Ensembl VEP and SnpEff, against ClinVar, gnomAD, dbSNP, dbNSFP and OMIM.
In-silico prediction
CADD, REVEL, SIFT, PolyPhen-2 and SpliceAI.
Classification
ACMG/AMP five-tier, from pathogenic to benign, with the evidence codes that produced each call.
Request a demo

Cancer panel analysis

CAN

Built for targeted cancer panels, where the questions differ from germline work: which variants are present, at what fraction, and which of them a report should actually carry.

Input

FASTQ or aligned BAM from targeted panels

Main analysis

Consensus calling, somatic variant detection, annotation and tiering

Output

Tiered variant report, annotated VCF, TMB and MSI status

Use model

Licensed to run on your own infrastructure

  1. FASTQpanel reads
  2. Alignto reference
  3. ConsensusUMI / duplex
  4. Somatic callMutect2, VarDict
  5. TierAMP/ASCO/CAP
  6. Reporttiered
Variant types
Somatic SNVs, indels, copy-number changes and gene fusions.
Modes
Tumour-normal and tumour-only, with UMI or duplex consensus calling for low allele fractions.
Callers
Mutect2, VarDict and LoFreq, tuned to panel depth rather than genome-wide assumptions.
Knowledge bases
COSMIC, OncoKB, CIViC, ClinVar and cBioPortal, with gnomAD used to filter germline background.
Signatures
Tumour mutational burden and microsatellite instability status.
Reporting
AMP/ASCO/CAP Tier I–IV significance categories, applied as a classification scheme.
Request a demo

Metagenomics & AMR

MetaXplore

From raw reads to a microbial profile. Taxonomic profiling and antimicrobial resistance detection in one pass, for samples where you do not know in advance what is in them.

Input

Shotgun metagenomic reads, or 16S / ITS amplicon data

Main analysis

Taxonomic profiling, AMR and virulence screening, assembly and binning

Output

Abundance tables, diversity metrics, AMR calls, Krona visualisations

Use model

Licensed to run on your own infrastructure

  1. FASTQshotgun / 16S
  2. QC & trimread filtering
  3. ProfileKraken2, MetaPhlAn
  4. AMR screenCARD, ResFinder
  5. AssembleMEGAHIT, binning
  6. Reportabundance & AMR
Input
Shotgun metagenomic reads, and 16S or ITS amplicon data.
Profiling
Kraken2 with Bracken abundance re-estimation, MetaPhlAn and Kaiju.
Reference databases
NCBI RefSeq and GTDB for shotgun; SILVA for 16S and UNITE for ITS.
AMR detection
CARD via RGI, ResFinder and NCBI AMRFinderPlus; VFDB for virulence factors.
Assembly
MEGAHIT and metaSPAdes, with MetaBAT2 binning and CheckM completeness checks.
Outputs
Abundance tables, alpha and beta diversity metrics, and Krona visualisations.
Request a demo

Questions

About the software

What input formats are supported?

All three tools start from FASTQ; 23rdExon and CAN also accept aligned BAM. MetaXplore takes shotgun metagenomic reads and 16S or ITS amplicon data.

Can we request a demo?

Yes. Tell us which tool you have in mind and roughly what your data looks like, and we will show it running on something close to your own case.

How does the software fit into an existing analysis workflow?

Each tool runs as a self-contained workflow from reads to report, so it can sit alongside what you already run rather than replacing it. Outputs are standard formats, so downstream tooling keeps working.

Are the three tools related?

No. 23rdExon, CAN and MetaXplore are independent tools built for different questions. You can license one without the others.

Is the software a diagnostic device?

No. These are analysis and interpretation tools for research and laboratory workflows. They are not certified diagnostic devices and their output is not a substitute for accredited diagnostic testing.

Would rather we ran the analysis instead? See our analysis services

Next step

Interested in our software?

Get in touch for a demo and pricing. Tell us which tool you have in mind and what your data looks like, and we will show you it running on something close to your own case.

Request a demo