NGLess

NGLess provides a domain-specific language for processing next-generation sequencing (NGS) data with emphasis on metagenomics, enabling analysis of shotgun metagenomes for characterization of microbial communities.

Key Features:

• Domain-specific language: A DSL for expressing NGS processing workflows focused on metagenomics analyses.
• Shotgun metagenome support: Explicit support for analysis of shotgun metagenomes from environmental samples.
• Sequence preprocessing: Implements standard sequence preprocessing operations on NGS data.
• Mapping to bundled databases: Performs mapping of reads to bundled databases for downstream analysis.
• Filtering of mapping results: Includes configurable filtering of mapping results.
• Taxonomic and functional profiling: Produces both taxonomic and functional profiles of metagenomic samples.
• Integration with external tools: Allows integration with external tools via configuration files.
• Pipeline construction and execution: Provides a framework for constructing and executing complex bioinformatics pipelines.
• Reproducibility: Enables reproducible computational pipelines; NG-meta-profiler built on NGLess is reported to maintain perfect reproducibility.
• NG-meta-profiler: Includes NG-meta-profiler, a high-performance metagenome profiler that streamlines preprocessing, mapping, filtering, and profiling.
• Performance comparison: NG-meta-profiler reports speed advantages relative to MOCAT2 and htseq-count.

Scientific Applications:

• Shotgun metagenome analysis: Analysis of shotgun metagenomes to characterize microbial community composition from environmental samples.
• Taxonomic profiling: Taxonomic profiling of microbial communities using mapped read data.
• Functional profiling: Functional profiling of metagenomes to characterize gene content and functional potential.
• High-throughput metagenomic profiling: High-performance metagenomic profiling workflows implemented via NG-meta-profiler.
• Reproducible pipeline development: Construction and execution of reproducible bioinformatics pipelines that integrate external tools via configuration files.

Methodology:

Sequence preprocessing, mapping to bundled databases, filtering of mapping results, and taxonomic and functional profiling; integration with external tools via configuration files.