MobiVision Quantify currently provides two cell filtering algorithms: CR2.2 and EmptyDrops (Lun et al., 2019, Genome Biology). Users can also specify the number of cells by using the --cellnumber INT parameter to select the top INT cells based on UMI count.

CR2.2 Algorithm: Barcodes aresorted by UMI count from high to low. If N is the expected number of cells(default is 3000), and m is the UMI count for the 99th percentile barcode,then all barcodes with UMI values greater than m/10 are identified ascells.

EmptyDrops Algorithm: Thisalgorithm further identifies cells with low RNA content, following apreliminary identification similar to CR2.2. It compares the RNA profileof these barcodes against a background model and identifies barcodes thatsignificantly deviate from the background as cells.