Outputs ======= The pipeline writes files using a common prefix (sample name). The prefix is either: - ``-o/--outprefix`` (if provided), or - derived from the input filename (basename without extensions) Main report artifacts --------------------- - ``_report.pdf`` - ``_report.json`` Haplotype FASTA outputs ----------------------- Common FASTA outputs include: - ``_cluster.fasta`` — high-frequency haplotypes - ``_lowFreqHap.fasta`` — low-frequency haplotypes - ``_chimeraHap.fasta`` — suspected chimeras BLAST output (optional) ----------------------- If BLAST is available: - ``_blast.tsv`` Distances --------- - ``_hapDistances.tsv`` — all-vs-all haplotype distance matrix Intermediate files ------------------ These are useful for debugging and reproducibility: - ``_subsample.fastq`` - ``_subsample.fasta`` - ``_mafftRaw.fasta`` - ``_mafft.log``