Pipeline to generate data and figures related to viral infection in the following work: "Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells" by Saikia, Burnham, et al., which is currently under review.
Files related to DART-seq technique including: A) Image_Analysis - scripts for fluorescence quantification of modified Dropseq beads. B) ViralInfections - Snakemake pipeline for host and virus transcription. Includes rules to identify viral fragments from T3D orthoreovirus and identify mutations. Will also generate figures related to paper. C) BcellRepertoire - Snakemake pipeline for host transcription in PBMCs, identification of B lymphocytes in PBMCs and subsequent determination of heavy and light chain elements. Will also generate figures related to the paper.