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¶
0.7.2¶
Added
min_distance
parameter tofragments
Fixed bug in soft clipping for
fragments
function
0.7.1¶
Code style update for
tagtotag
andtagtorg
Fix bug in
filterbarcodes
andaddtags
that caused lines in BAM header to be duplicated (https://github.com/timoast/sinto/issues/15)
0.7.0¶
New
tagtotag
function to copy or move read tags
Version 0.6¶
0.6.1¶
Bug fixes for
barcode
functionAllow running
barcode
on unzipped FASTQ files
0.6.0¶
New
barcode
function to add cell barcodes to read names in FASTQ file
Version 0.5¶
0.5.1¶
Fix bug in
utils.read_cell_barcode_file
when same cell appears on multiple lines
0.5.0¶
Add
tagtorg
command to add read groups to BAM according to cell barcode.
Version 0.4¶
0.4.3¶
Throw error if file is not present for
filterbarcodes
andaddtags
0.4.2¶
Fix bug when cell barcode is None for
fragments
function.
0.4.1¶
Increase recursion limit to prevent error when running on genomes with >1000 scaffolds.
0.4.0¶
Removed
sam
parameter fromfilterbarcodes
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¶
0.3.4¶
Memory improvements for
fragments
function
0.3.3¶
Bug fix for
fragments
function when using chromosome containing zero fragments
0.3.2¶
Added
--barcodetag
and--barcode_regex
arguments tofilterbarcodes
0.3.1¶
Better handling of BAM file opening/closing
Add
max_distance
parameter tofragments
to remove fragments over a certain length
0.3.0¶
added
fragments
function to create scATAC fragment file from BAM fileremoved use of versioneer for version tracking
Version 0.2¶
added
addtags
function to add read tags to BAM file for different groups of cells