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23rd Pair Lab Limited

Software

Software we build
and run ourselves

Analysis tools built for the questions we get asked most. Each one takes raw sequencing data and carries it 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.

  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 are different from germline work: which variants are present, at what fraction, and which of them a report should actually carry.

  1. FASTQpanel reads
  2. Alignto reference
  3. ConsensusUMI / duplex
  4. Somatic callMutect2, VarDict
  5. TierAMP/ASCO/CAP
  6. Reportclinical
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 clinical significance.
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.

  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

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.

Contact us for a demo and pricing