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Getting started

AMALGKIT is a Python-only toolkit for transcriptome amalgamation across studies and species. Current releases do not require R or any R packages.

• Installation and dependencies
• Parallel processing
• Tutorial 1

Active commands

• amalgkit dataset: extract bundled test datasets
• amalgkit metadata: retrieve and organize SRA metadata
• amalgkit integrate: add local FASTQ files to metadata
• amalgkit select: mark samples for downstream analysis using select_rules.tsv
• amalgkit getfastq: download or prepare FASTQ files
• amalgkit quant: quantify transcript abundance with kallisto or oarfish
• amalgkit merge: merge per-run abundance tables by species
• amalgkit busco: prepare BUSCO tables for downstream ortholog-based steps
• amalgkit cstmm: cross-species TMM normalization using single-copy genes
• amalgkit wsfilter: within-species outlier filtering
• amalgkit csfilter: cross-species outlier filtering
• amalgkit finalize: export final expression tables, summaries, and batch-corrected outputs
• amalgkit sanity: check expected pipeline outputs
• amalgkit rerun: rerun failed targets recorded by sanity

Typical pipeline

amalgkit dataset --rule_set base --out_dir ./ --overwrite yes
amalgkit metadata --out_dir ./ --search_string 'YOUR_QUERY'
amalgkit select --out_dir ./
amalgkit getfastq --out_dir ./
amalgkit quant --out_dir ./
amalgkit merge --out_dir ./
amalgkit cstmm --out_dir ./ --dir_busco ./busco        # optional
amalgkit wsfilter --out_dir ./                         # optional
amalgkit csfilter --out_dir ./ --dir_busco ./busco      # optional
amalgkit finalize --out_dir ./

finalize supports Python backends for no, sva, ruvseq, combatseq, and latent_glm.

Legacy command migration

Old command	Current workflow
amalgkit config	amalgkit dataset --rule_set ... writes select_rules.tsv; edit that file before amalgkit select
amalgkit curate	run amalgkit wsfilter, optionally amalgkit csfilter, then amalgkit finalize
amalgkit csca	use amalgkit csfilter for cross-species filtering and amalgkit finalize for final tables and plots