Entourage

Entourage streamlines virome investigation through a single workflow enabling short-read assembly, virus identification, and intrasample sequence variation profiling.

Key Features:

• Short-read sequence assembly: Assembles short-read sequence data as part of end-to-end virus sequence detection analysis.
• Viral sequence search with reference targets: Searches for viral sequences using contig-based approaches with reference virus targets.
• Viral sequence search without reference targets: Searches for viral sequences using contig-based approaches without reference virus targets.
• Intrasample sequence variation quantification: Quantifies virus intrasample genetic variations and generates publication-quality figures illustrating the results.
• Read cleaning: Processes raw sequence reads for quality control as part of the virus detection workflow.
• Comprehensive results generation: Produces results allowing for thorough quality control, reliability assessment, and interpretation.

Scientific Applications:

• Target virus detection: Comprehensively searches for target virus sequences in raw sequence read data from samples such as HeLa cell culture spiked with viruses.
• Novel virus discovery: Discovers novel viruses effectively, performing well even with low virus sequencing depth in single digits.
• Virome investigation of environmental datasets: Analyzes preassembled metagenomic datasets such as the Tara Oceans dataset for viral sequences.
• Chronic infection genetic variation analysis: Quantifies intrasample genetic variations in sequence data from patients with chronic SARS-CoV-2 infection.

Methodology:

Several workflows are implemented to facilitate end-to-end virus sequence detection analysis through a single command line, from read cleaning, sequence assembly, to virus sequence searching using contig-based approaches.