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amalgkit finalize

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Kenji Fukushima edited this page Jun 8, 2026 · 3 revisions

Overview

amalgkit finalize exports final per-species tables from filtered metadata. It is Python-only and is the current place for optional batch correction.

Input

  • --metadata: usually wsfilter/metadata.tsv or csfilter/metadata.tsv
  • --input_dir: merge or cstmm output directory

If --metadata inferred is used, finalize automatically picks the newest of:

  • out_dir/wsfilter/metadata.tsv
  • out_dir/csfilter/metadata.tsv
  • otherwise out_dir/metadata/metadata.tsv

Batch-correction backends

--batch_effect_alg supports:

  • no
  • sva
  • ruvseq
  • combatseq
  • latent_glm

All backends are implemented in Python in current releases.

Example

No batch correction:

amalgkit finalize --out_dir ./ --metadata ./csfilter/metadata.tsv --batch_effect_alg no

Nonnegative latent-factor correction:

amalgkit finalize \
    --out_dir ./ \
    --metadata ./csfilter/metadata.tsv \
    --batch_effect_alg latent_glm \
    --latent_family nb \
    --latent_k auto

Main outputs

Top level:

  • finalize/metadata.tsv
  • finalize/finalize_exclusion.pdf

Per species:

  • <Species>_metadata.tsv
  • <Species>_expression.tsv
  • <Species>_expression_uncorrected.tsv
  • <Species>_sample_group_mean.tsv
  • <Species>_sample_group_mean_uncorrected.tsv
  • <Species>_tau.tsv
  • <Species>_correlation_statistics.tsv
  • <Species>_batch_effect_summary.tsv
  • <Species>_curation_round_summary.tsv
  • <Species>_curation_final_summary.tsv
  • <Species>_batch_compare_<alg>.pdf
  • <Species>_tau_hist_<alg>.pdf

Useful options

General:

  • --norm
  • --clip_negative
  • --maintain_zero
  • --seed

SVA:

  • --sva_nsv
  • --sva_B
  • --sva_B_auto_max

RUVSeq:

  • --ruvseq_control_genes
  • --ruvseq_k
  • --ruvseq_k_max

latent_glm:

  • --latent_family poisson|nb
  • --latent_k INT|auto
  • --latent_k_max INT
  • --latent_max_iter INT
  • --latent_tol FLOAT

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