Essential parameters

These are the parameters most users will care about.

Input

input_fastq: input FASTQ file (.fastq/.fq, optionally gzipped)

Output naming

--outdir: output directory (default: current directory)
-o / --outprefix: output prefix / sample name (default: input basename)

Read filtering / subsampling

--min-meanq: minimum mean Q-score per read (default: 30)
--sample: number of reads to subsample after filtering (default: 5000)
--seed: random seed (default: 420)

Alignment (MAFFT)

--mafft: path to MAFFT executable (default: mafft)
--threads: MAFFT thread count (default: 30)

Reproducibility

--force: ignore existing intermediate files and recompute (default: off)