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Welcome to the C-BIRD wiki!

The C-BIRD is a pipeline designed to address clinical needs for identifying a pathogenic organism and its possible antibiotic resistance using whole genome sequencing (WGS) data, especially in hospital-acquired infections. It is developed to comply with the CLIA requirements. Versions of all programs, tools, and databases used are logged in this manner. Also, automatic update of any program or database is turned off deliberately for the complete control of the analysis workflow. The pipeline makes a de novo assembly from Illumina paired-end reads. The pipeline reports QC metrics of assembly. Species, MLST type, antimicrobial resistance genes, stress genes, hypervirulence genes, plasmids, plus any targeted gene are detected and reported by the pipeline.

C-BIRD is written in Workflow Description Language (WDL). It runs on a web-based platform TERRA and the command line. C-BIRD performs:

• Adapter removal, quality filtering, and base trimming
• PhiX cleaning
• Normalization (disabled in default)
• Taxonomic profiling of reads (for contamination screening)
• De Novo assembly
• Assembly evaluation
• Genomic data quality assessment
• Bacterial identification
• MLST Typing
• Antimicrobial resistance, stress, and hypervirulence gene detection
• Target gene search
• Plasmid detection
• Individual summary report generation

In addition to the main workflow, C-BIRD has some extras, such as a wrapper workflow and scripts for the command line (multiBIRD) and a workflow estimating insert size distribution.

Please check the dependencies and installation pages for more information.