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

• Copy cell barcodes to/from read names or read tags

• 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 0.10

0.10.1

• Fixed bug in gzip file loading (https://github.com/timoast/sinto/issues/67)

• Fixed NoneType errors in barcode function (https://github.com/timoast/sinto/pull/65; @bgruening)

0.10.0

• Add ability to perform barcode correction in barcode (https://github.com/timoast/sinto/pull/61; @dawe)

Version 0.9

0.9.0

• Add blocks command to create block file from BAM file.

Version 0.8

0.8.4

• Include unmapped reads in output of filterbarcodes (https://github.com/timoast/sinto/issues/55)

0.8.3

• Fixed bug in BAM file chunking that caused some entries to be duplicated (https://github.com/timoast/sinto/issues/51)

• Properly set minimum Python version (https://github.com/timoast/sinto/issues/53)

• Fix bug in filterbarcodes when no RG tags in BAM file (https://github.com/timoast/sinto/issues/52)

0.8.2

• Fixed bug in filterbarcodes when cell barcode in the middle of the read name (https://github.com/timoast/sinto/issues/46)

0.8.1

• Fixed bug in nametotag when cell barcode in the middle of the read name (https://github.com/timoast/sinto/issues/46)

• Remove need for samtools in path (https://github.com/timoast/sinto/issues/41)

• Added --outdir parameter to filterbarcodes

• Added --sam parameter to filterbarcodes

• Fixed bug in filterbarcodes and addtags causing read groups to be modified (https://github.com/timoast/sinto/issues/17)

0.8.0

• Added tagtoname and nametotag commands to copy cell barcodes to/from read tags or read names

Version 0.7

0.7.6

• Added --collapse_within parameter to fragments function to enable only collapsing PCR duplicates if the cell barcode is the same (https://github.com/timoast/sinto/issues/36)

• Added tests for fragments function and associated small test dataset

0.7.5

• Added --shift_plus and --shift_minus parameters to configure Tn5 shift applied in fragments function (https://github.com/timoast/sinto/issues/33)

0.7.4

• Fixed bug causing some fragments at the end of contigs to be dropped (https://github.com/timoast/sinto/issues/31)

0.7.3

• Fixed error in soft clipping for fragments function (https://github.com/timoast/sinto/issues/29)

0.7.2

• Added min_distance parameter to fragments

• Fixed bug in soft clipping for fragments function

0.7.1

• Code style update for tagtotag and tagtorg

• Fix bug in filterbarcodes and addtags 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 function

• Allow 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 and addtags

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 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

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 to filterbarcodes

0.3.1

• Better handling of BAM file opening/closing

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

0.3.0

• 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