Donor assignment / doublet detection tools in support of Cell Stem Cell publication

[jamesnemesh]

This release is in support of our manuscript "Natural variation in gene expression and viral susceptibility revealed by neural progenitor cell villages" by Wells, et al., which has been accepted for publication in Cell Stem Cell. The following software is relevant for release.

• AssignCellsToSamples - This program takes as input a BAM file containing sequencing reads from a pool of donors, and a VCF file containing genotypes from those donors. The program emits the most likely donor for each cell.
• DetectDoublets - This program takes as input a BAM file containing sequencing reads from a pool of donors, a VCF file containing genotypes from those donors, and the output from AssignCellsToSamples. The program emits the probability that each cell barcode is a doublet where a cell from two different donors have been co-encapsulated in the same droplet.
• TagReadWithGeneFunction - This program adds additional gene function tags to a BAM file that are required to run donor assignment code. This programs are run as part of the standard Drop-seq pipeline, but can also be run on standard 10x BAM files to make them compatible with our toolkit. Please see the Drop-seq alignment cookbook and command line help for details.

Please also see our biorxiv manuscript Natural variation in gene expression and Zika virus susceptibility revealed by villages of neural progenitor cells which is already available. We will publish a computational protocols guide in support of this work in the following weeks.

See the Drop-seq alignment cookbook and Census-seq computational protocols for detailed usage instructions, diagrams, and explanations of how these new systems work. For more information about Census-seq, see our manuscript on bioRxiv

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