Bioinformatics Analysis

Overview

The DRY-lab of the Biomics platform propose bioinformatics analysis as part of our service. All service analysis are performed with the Sequana project.

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RNA-seq

  • Data: Illumina or MGI. Paired or not, 50, 75, 150bp.
  • Requirements: a genome and its annotation. Usually a NCBI accesion but we can also use custom reference.
  • Analysis:
    • trimming: low quality and adapter removal
    • mapping: star/bowtie2 depending on the input data
    • QCs (e.g. ribosomal content)
    • taxonomy
  • Deliverables:
    • Quality assessments for all samples before/after trimming
    • Quality of mapping and assignation (read metrics mapping)
    • Ribosomal content for bacterial genomes
    • PCA analysis
    • list of differentially expressed genes including fold change and adjusted p-values
    • files with raw counts and normalized counts
    • BAM and bigwig files on requests
    • HTML reports
  • Collaboration mode:
    • Enrichment:
      • KEGG enrichment
      • GO terms enrichment
    • Mapping rate of pathogen
    • custom analysis

Bacterial genome assembly (short read)

  • Data Illumina/MGI e.. PE150, PE300
  • Requirements: a genome and its annotation (optional). Usually a NCBI accesion but we can also use custom reference.
  • Analysis:
    • trimming: low quality and adapter removal
    • Assembly
    • Quality assessments
    • Annotation
  • Deliverables:
    • assembly fasta file,
    • contig coverage plots
    • quality assessments for all samples,
    • BUSCO identification of core genome.
    • HTML reports

Long read assembly

  • Data: Pacbio / Nanopore
  • Requirements: none.
  • Analysis:
    • Error correction
    • Assembly
    • Quality assessments
    • Annotation
  • Deliverables:
    • assembly fasta file,
    • contig coverage plots
    • quality assessments for all samples,
    • BUSCO identification of core genome.
    • HTML reports

Variant calling

  • Data: Illumina or long reads
  • Requirements: a genome and its annotation (optional). Usually a NCBI accesion but we can also use custom reference.
  • Analysis:
    • trimming: low quality and adapter removal
    • Mapping
    • Variant calling (freebayes)
  • Deliverables:
    • VCF files with SNP and INDELs
    • HTML reports

Long Amplicon Analysis (Long read)

This is currently only in collaboration mode

ChIP-seq

This is currently only in collaboration mode

Cut&Tag

This is currently only in collaboration mode

Taxonomy

  • Data: Illumina or long reads
  • Analysis:
    • taxonomic assignment using various databases (viruses, bacterial, eukaryotes, etc)
  • Deliverables:
    • CSV files
    • HTML reports

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