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Bioinformatic Workflows

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  • Genomics

  • Genome assembly
  • Variant analysis
  • Metagenomics
  • Genetic analysis

  • Transcriptomics

  • Exploratory gene expression analysis
  • RNA-seq analysis
  • Pathway analysis
  • Transcriptome assembly
  • Single-cell expression analysis
  • MicroRNA data analysis
  • Alternative splicing analysis
  • Fusion gene detection

    • Pipeline for the alignment of short reads (< 1000 bp)

    This pipeline performs the alignment of fastq files, from DNA sequencing reads, using BWA-MEM. It is recommended for reads with and mean length greater or equal to 70 bp and below 1000 bp.

    What you should provide

    1. Reads in fastq format (ideally compressed in .gz format)
    2. The organism from which they come from.

    What you will receive

    1. File with the aligned reads in BAM format.
    2. File with alignment statistics.

    WARNING: These files are required for followup analysis, such as Small variant analysis, Copy number variants, Structural variants. Visual exploration of the BAM genomic data can be assessed in IGV.

    Software versions

    • BWA v0.7.17
    • Samtools v1.15.1
    • BioBamBam2 v2.0.87
    • GATK v4.3.6.1

    Relevant software values (assume default if unspecified)

    • None

    Pipeline 🔗

    Methods (Please adapt)

    Mapping to reference genome (assembly version XXX) was performed using BWA mem (version 0.7.17) and duplicates were removed using biobambam2 (version 2.0.87) followed by base quality recalibration using GATK (version 4.3.6.1).