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Getting started

Installation and dependencies

Parallel processing

Functions

• amalgkit metadata: NCBI SRA metadata retrieval and curation

• amalgkit integrate: Appending local fastq info to a metadata table

• amalgkit config: Creating a series of config files for the metadata selection

• amalgkit select: Selecting SRA entries for analysis

• amalgkit getfastq: Generate fastq files

• amalgkit quant: Transcript abundance estimation

• amalgkit merge: Generating transcript abundance tables

• amalgkit cstmm: Cross-species TMM normalization using single-copy genes

• amalgkit curate: Automatic removal of outlier samples and unwanted biases

• amalgkit csca: Generating plots with cross-species correlation analysis

• amalgkit sanity: Checking the integrity of AMALGKIT input and output files