Sinto: single-cell analysis tools

Sinto is a toolkit for processing aligned single-cell data. Sinto includes functions to:

  • Subset reads from a BAM file by cell barcode

  • Create a scATAC-seq fragments file from a BAM file

  • Add read tags to a BAM file according to cell barcode information

Report issues and view source code here.

Major version changes indicate new functionality or breaking changes to existing functionality.

Minor version changes indicate bug fixes or performance improvements to existing functionality without breaking compatibility with previous versions.

Version 0.4


  • Removed sam parameter from filterbarcodes

  • Allow multiple groups of cells to be specified in filterbarcodes. This will create a separate BAM file for each unique group of cells.

Version 0.3


  • Memory improvements for fragments function


  • Bug fix for fragments function when using chromosome containing zero fragments


  • Added --barcodetag and --barcode_regex arguments to filterbarcodes


  • Better handling of BAM file opening/closing

  • Add max_distance parameter to fragments to remove fragments over a certain length


  • added fragments function to create scATAC fragment file from BAM file

  • removed use of versioneer for version tracking

Version 0.2

  • added addtags function to add read tags to BAM file for different groups of cells

Version 0.1

First release. Functionality:

  • filterbarcodes