Biomics Dry-lab Group (2018-2024)

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.

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

links

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