For Illumina: Drop paired or single fastq.gz files here
For Nanopore: Drop pod5 or BAM files here
Accepted formats: .fastq.gz (Illumina) | .pod5, .bam (Nanopore)
Select sequencing type:
 
Select the background genome:
 
Select the primary genome:
 
Amount of file to use (% to subset; only for fastq.gz files):  
 
 

Paired-End Read Reference Pipeline Overview

  • Sequential alignment to human and MTB genomes
  • Optimized parameters for bacterial alignment
  • Tracking of unaligned reads between references

  • Comprehensive alignment statistics
  • MultiQC report generation
  • R-based visualization of results
  • Comparative analysis between references

  • Automatic cleanup of intermediate files
  • Organized output structure
  • Summary statistics compilation
  • Email delivery of results