isolateR

isolateR generates microbial strain libraries from Sanger sequencing data through automated batch processing, taxonomic classification via global alignment to type strain databases, and customizable dereplication of clonal isolates.

Key Features:

• Automated Batch Processing: Processes Sanger sequence files in batches without manual intervention.
• Taxonomic Classification: Classifies sequences via global alignment to type strain databases following latest international nomenclature standards.
• Strain Library Creation: Creates strain libraries with customizable sequence dereplication thresholds and combines data from multiple sequencing runs into a single library.
• Clonal Isolate Handling: Manages clonal isolates during library generation.
• Interactive HTML Outputs: Generates interactive HTML outputs for data exploration and analysis.

Scientific Applications:

• Microbial Diversity Cataloging: Catalogs microbial diversity through generation of culture collections with strain-level resolution.
• Novel Species Discovery: Facilitates discovery of novel species by processing taxonomic marker genes including 16S, 18S, ITS, rpoB, and cpn60 from bacteria, archaea, and fungi.
• Human Gut Microbiome Analysis: Benchmarked on human gut genome catalogues including IMGG and Hadza hunter-gatherer populations for targeted strain-level exploration within individual hosts.

Methodology:

isolateR implements a three-step pipeline: (1) automated batch processing of Sanger sequence files, (2) taxonomic classification via global alignment to type strain databases in accordance with the latest international nomenclature standards, and (3) creation of strain libraries with customizable sequence dereplication thresholds and combination of data from multiple sequencing runs.