Mature pipeline

• Flexible de-multiplexing: remove primers, extract UMIs from adapters, positional UMI extraction, pre-processed data (UMI in header)
• CLI supports both manual (FASTQ pair) and project (set up via json) scale analysis
• Supports tabular, binary and VCF/SAM output
• Alignment is performed using hybrid k-mer + SmithWaterman algorithm, selected for its accuracy as MIG assembly greatly decreases the number of mappings required. MAPQ score is computed as k-mer overlap information measure
• Probabilistic error model for variant quality based on background error frequency