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This method is also similar to the default method in the Drop-seq cookbookAlignment Cookbook (Macosko et al. 2015), which collapses UMI barcodes with a Hamming distance of 1. 

This method may output more UMIs than the default behavior as only UMIs within an edit distance of 1 are summarized, whereas UMIs with a greater distance can be linked in the UMI-tools method. For a comparison of the performance of the two approaches, please see the Adjacency (CellRangerCell Ranger) and Directional (UMI-tools) methods described in Smith et al. 2017. 

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Connor, University of Michigan BRCF Bioionformatics Core https://pypigithub.org/projectcom/umich-brcf-bioinf/Connor/

Cell Ranger Algorithms Overview, 10X Genomics https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/algorithms/overview

Drop-seq Alignment Cookbook v1.2 Jan 2016, James Nemesh, Steve McCarroll’s lab, Harvard Medical School  http://mccarrolllab.com/wp-content/uploads/2016/03/Drop-seqAlignmentCookbookv1.2Jan2016.pdf

Macosko E, Basu A, Satija R, et al. Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Cell 2015; 161(5):1202-1214. https://doi.org/10.1016/j.cell.2015.05.002