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:
Illumina Paired-End
Illumina Single-End
Nanopore
Nanopore Multiplexed
Select the background genome:
human
mouse
Select the primary genome:
H37Rv
Salmonella_typhimurium_SL1344
Amount of file to use (% to subset; only for fastq.gz files):
Is DNA
Keep BAM files in output
Keep input files after processing
Submit
PERRP Pipeline Description
Paired-End Read Reference Pipeline Overview
1. Dual Reference Alignment
Sequential alignment to human and MTB genomes
Optimized parameters for bacterial alignment
Tracking of unaligned reads between references
2. Analysis and Statistics
Comprehensive alignment statistics
MultiQC report generation
R-based visualization of results
Comparative analysis between references
3. Output Processing
Automatic cleanup of intermediate files
Organized output structure
Summary statistics compilation
Email delivery of results