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

• <prefix>_report.pdf

• <prefix>_report.json

Haplotype FASTA outputs

Common FASTA outputs include:

• <prefix>_cluster.fasta — high-frequency haplotypes

• <prefix>_lowFreqHap.fasta — low-frequency haplotypes

• <prefix>_chimeraHap.fasta — suspected chimeras

BLAST output (optional)

If BLAST is available:

• <prefix>_blast.tsv

Distances

• <prefix>_hapDistances.tsv — all-vs-all haplotype distance matrix

Intermediate files

These are useful for debugging and reproducibility:

• <prefix>_subsample.fastq

• <prefix>_subsample.fasta

• <prefix>_mafftRaw.fasta

• <prefix>_mafft.log