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

  • Add read groups based on read tags

  • Copy or move read tags to another read tag

  • Add cell barcodes to FASTQ read names

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 0.7


  • Added min_distance parameter to fragments

  • Fixed bug in soft clipping for fragments function



  • New tagtotag function to copy or move read tags

Version 0.6


  • Bug fixes for barcode function

  • Allow running barcode on unzipped FASTQ files


  • New barcode function to add cell barcodes to read names in FASTQ file

Version 0.5


  • Fix bug in utils.read_cell_barcode_file when same cell appears on multiple lines


  • Add tagtorg command to add read groups to BAM according to cell barcode.

Version 0.4


  • Throw error if file is not present for filterbarcodes and addtags


  • Fix bug when cell barcode is None for fragments function.


  • Increase recursion limit to prevent error when running on genomes with >1000 scaffolds.


  • 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