Influenza A virus undergoes compartmentalized replication in vivo dominated by stochastic bottlenecks.
Amato KA, Haddock LA, Braun KM, Meliopoulos V, Livingston B, Honce R, Schaack GA, Boehm E, Higgins CA, Barry GL, Koelle K, Schultz-Cherry S, Friedrich TC, Mehle A.
This repository stores the scripts used to obtain and analyze barcode and whole genome sequences from our barcoded Influenza A Virus study.
The generation of barcodes and barcode frequencies from paired end fastq files (Illumina) were obtained using the following packages:
- Merged (BBTools)
- Mapped (BBTools)
- Trimmed (BBTools)
- Aligned and Sorted (Samtools)
- Barcode extraction (Command Line toools)
- Barcode Clustering (UMITools)
To cite this work, please use:
Amato KA, Haddock LA, Braun KM, Meliopoulos V, Livingston B, Honce R, Schaack GA, Boehm E, Higgins CA, Barry GL, Koelle K, Schultz-Cherry S, Friedrich TC, Mehle A. 2022. Influenza A virus undergoes compartmentalized replication in vivo dominated by stochastic bottlenecks. Nature Communications 13:3416.