Please drop the fastq.gz files here.
Separate files will be treated as separate samples (exc. paired files)
Select an assay: 


Generic Alignment Pipeline Overview

  • Supports both Illumina and Nanopore data
  • Automatic detection of sequencing platform
  • Platform-specific alignment strategies

  • BWA-MEM for Illumina paired-end reads
  • Minimap2 for Nanopore long reads
  • Multi-threaded processing for speed
  • Generates sorted and indexed BAM files

  • BCFtools mpileup for initial variant detection
  • Freebayes as secondary variant caller
  • Depth of coverage analysis
  • Large INDELS
  • IS6110 insert positions
  • Comprehensive VCF output

  • R-based plotting of coverage and variants
  • Gene-level annotation of variants
  • Interactive visualization outputs
  • Results delivered via email