For Illumina: Drop paired fastq.gz files here (multiple files will be treated as a seperate samples)
For Nanopore: Drop pod5 or BAM files here
Accepted formats: .fastq.gz (Illumina) | .pod5, .bam (Nanopore)
Select an assay:
Illumina PE
Nanopore
Nanopore Multiplexed
Keep BAM files in output
Keep input files after processing
Submit
Generic Pipeline Description
Generic Alignment Pipeline Overview
1. Input Processing
Supports both Illumina and Nanopore data
Automatic detection of sequencing platform
Platform-specific alignment strategies
2. Alignment Processing
BWA-MEM for Illumina paired-end reads
Minimap2 for Nanopore long reads
Multi-threaded processing for speed
Generates sorted and indexed BAM files
3. Variant Analysis
BCFtools mpileup for initial variant detection
Freebayes as secondary variant caller
Depth of coverage analysis
Large INDELS
IS6110 insert positions
Comprehensive VCF output
4. Visualization and Reporting
R-based plotting of coverage and variants
Gene-level annotation of variants
Interactive visualization outputs
Results delivered via email