AMULET v1.1

This release adds code to skip comment lines in fragment files from Cell Ranger ATAC 2.0.

The restriction list sites can be downloaded from the previous release. Alternatively these files can be obtained by combining restriction sites (tab delimited chr star end file format) from ENCODE with repetitive elements such as simple repeats and segmental duplications from RepeatMasker/UCSC Genome Browser.

AMULET v1.0

This is the first release since renaming the tool from ATAC-DoubletDetector to AMULET. This release provides the following:

1. The ability to detect multiplets using fragment files
2. Additional options for adjusting the expected overlap threshold and adjusting the bases from reads.
3. Numerous bug fixes

Note: The outputs between using alignments (e.g., possorted.bam) and the fragment files (fragments.tsv.gz) may be slightly different due to additional processing performed on the fragment files.

ATAC-DoubletDetector v1.1-beta

This release adds an additional option to force processing a bam file when the file is not recognized as coordinate sorted.

Additionally, mapping quality and max insert size thresholds can now bet set as optional parameters.
The default cell_id column has been changed to be the same as barcode (column index = 0), as the latest CellRangerATAC pipeline no longer assigns cell ids to cells and instead just provided barcodes as the unique identifiers.

Combined sites designating blacklist, segmental duplications and repetitive elements can be downloaded from the 1.0-beta release.

ATAC-DoubletDetector v1.0-beta MIT License

This release provides code and jar binaries to detect doublets. These jar files should work as long as an appropriate version of java is installed on the system to run them.

Note: This release includes all source code that can be released under the MIT license. Future releases that include scripts for annotating doublets will need to be released under a GPL license due to its use of R scripts (which is more restrictive for any future development when using these libraries in conjunction with apache libraries for example).