What We Can Do For You

NGS Analysis

Data Pre-processing

We check the quality of raw reads and prepare them for downstream analysis.

Analysis Steps

• Quality filtering
• Adapter trimming
• Discarding rRNA-mapped reads or contaminants

Output Files

• Quality report (HTML/PDF)
• Filtered reads in FASTQ format

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RNA-Seq

Expression Analysis

We estimate gene and transcript expression, then compare it between conditions.

Analysis Steps

• Gene/transcript expression estimation
• Differential expression analysis
• KEGG pathway and GO enrichment analysis

Output Files

• Expression tables (FPKM/RPKM/TPM)
• DE gene lists with fold changes
• Heatmaps, MA and volcano plots

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RNA-Seq

Ab initio Transcriptome Assembly

We assemble the transcriptome against a reference genome to detect novel genes and splicing isoforms. On request we also annotate the assembled transcriptome.

Analysis Steps

• Read mapping against reference genome
• QC and post-processing
• Novel gene and isoform detection

Output Files

• Quality report
• Transcriptome in GFF/GTF and FASTA
• Sashimi plots on request

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RNA-Seq

De novo Transcriptome Assembly

We assemble the transcriptome without a reference, so no genome sequence is needed. On request we add annotation: identification of homologous proteins and long non-coding RNAs.

Analysis Steps

• De novo assembly
• Quality measures calculation

Output Files

• Transcriptome in FASTA format
• Quality report

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Annotation

Transcriptome Annotation

We identify protein-coding genes and ncRNAs, assign GO terms and KEGG pathways, and identify domains.

Analysis Steps

• Protein-coding gene identification
• Protein domain and homolog identification
• KEGG/GO assignment
• ncRNA identification (lncRNA, circRNA, miRNA)

Output Files

• Tab-delimited annotation file
• FASTA and GFF/BED files

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Small RNA

Small RNA Analysis

We identify and quantify miRNAs and siRNAs, and predict their target genes.

Analysis Steps

• miRNA and phased siRNA identification
• Differential expression
• IsomiR and RNA editing analysis
• Target identification

Output Files

• Expression profiles
• Target predictions
• miRBase upload

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Proteomics

Proteomics and Peptidomics

We analyse mass spectrometry data — from sample preparation support to biological interpretation.

Analysis Steps

• Quality control
• Protein/peptide identification (DB search + de novo)
• Quantitative LC/MS processing
• DIA/SWATH analysis

Output Files

• Quantification results
• Statistical analysis
• Visualisations

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Genomics

Genome Variant Calling

We detect SNPs, short indels and structural variants in sequencing data.

Analysis Steps

• Germline and somatic alteration detection
• Analysis of WGS, Exome-Seq and targeted sequencing data

Output Files

• Annotated VCF files
• Variant reports

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Genomics

De novo genome assembly — bacteria

We assemble and annotate bacterial genomes, reaching a closed chromosome with its plasmids, and screen for resistance and virulence genes.

Analysis Steps

• Assembly from short, long or hybrid reads
• Polishing and closure assessment
• Structural and functional annotation
• Detection of resistance and virulence genes and of plasmids

Output Files

• Genome and plasmids in FASTA
• GFF3 and GenBank annotation
• Annotation and strain characterisation spreadsheet

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Genomics

De novo genome assembly — eukaryotes

We assemble plant, animal and fungal genomes from long reads, order them with Hi-C data and annotate genes using RNA-Seq.

Analysis Steps

• Genome size, heterozygosity and ploidy assessment
• Contig assembly and chromosome-level scaffolding
• Repeat identification and masking
• Structural and functional gene annotation

Output Files

• Genome in FASTA and GFF3 annotation
• Proteins and coding sequences
• BUSCO, Merqury and QUAST reports
• Genome browser configuration

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Other NGS

Other NGS Analyses

We analyse ChIP-Seq data, study RNA editing and alternative splicing, and deposit data in public repositories.

Analysis Steps

• ChIP-Seq (Pol II, histone modifications)
• RNA editing event detection
• Alternative splicing analysis

Output Files

• Analysis reports
• SRA/GEO data upload

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Infrastructure

Linux server account

We provide a ready-to-use computing environment with the software installed, for when you prefer to analyse the data yourself.

Analysis Steps

• An account on our server with SSH access
• Installation and configuration of tools for your type of analysis
• Disk space matched to the size of your data
• Support when you first run the pipeline

Output Files

• Access details and a short getting-started guide
• A prepared environment (conda/modules) with a list of tool versions

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Infrastructure

Custom software and databases

We build dedicated pipelines, web applications and biological databases for a specific research project.

Analysis Steps

• Requirements and scope agreed with the research team
• Building the pipeline or application, under version control
• Deployment on your server or on ours
• Documentation and handover of the code

Output Files

• Source code in a repository, with documentation
• A working deployment and a maintenance guide

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Design

Primer and Probe Design

We design custom PCR/qPCR primers and probes, and validate their specificity.

Analysis Steps

• PCR/qPCR primer design
• Custom qPCR probe design
• Specificity checking

Output Files

• Optimized primer/probe sequences

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