READemption

READemption processes RNA-Seq data to perform quality control, alignment, read quantification, and differential expression analysis for transcriptomic studies.

Key Features:

• Implementation: Implemented in Python.
• Comprehensive integration: Consolidates quality control, alignment, read quantification, and differential expression analysis within a single pipeline.
• Parallel processing: Supports parallel processing in most subcommands to accelerate computation.
• Sample versatility: Applicable to bacterial primary transcriptomes, whole transcriptomes, protein-immunoprecipitated reads, and samples from eukaryotes and archaea.

Scientific Applications:

• Gene expression profiling: Detection and quantification of transcript abundance across samples using RNA-Seq data.
• Differential expression analysis: Identification of differentially expressed genes between conditions.
• Transcriptome characterization: Analysis of primary transcriptomes and protein-associated RNAs across bacteria, eukaryotes, and archaea.

Methodology:

Performs quality control, alignment, read quantification, and differential expression analysis within a Python-based pipeline with support for parallel execution.