UniverSC Version 1.1.7

12 November 2021

• uses reverse complement barcode whitelist for inDrops v1 and v2 (automatically generated)

• updated matching to remove adapter sequence between barcodes tested locally

• updates to support legacy versions (v1 and v2) of inDrops protocol

• documents GUI application

• documents pre-generated references

• updates large files in Docker image

Full Changelog: 1.1.6...1.1.7

UniverSC Version 1.1.6

26 September 2021

• update building STAR in Docker containers

• updates to syntax in script and subroutines

• bug fixes to allow running without --verbose parameters

• minor updates to documentation for added technologies

Graphical applications (GUI-based UniverSC) are provided as binaries.

UniverSC Version 1.1.5

2 September, 2021

• add subroutine to support custom references

• update Docker build parameters

• supports application with graphical user interface

UniverSC Version 1.1,4

30 July, 2021

• add test data for Smart-Seq3

• update handing chemistry in set up

• correct STAR in docker container

UniverSC Version 1.1.3

29 June, 2021

• update paths for compatibility with Red Hat Linux (Fedora and CentOS)

• bug fixes for subroutines (SmartSeq3 processing)

• bug fixes for arithmetic operations

• updated documentation

UniverSC Version 1.1.2

1 June, 2021

• bug fixes for aligent parameters

• update paths to call subroutines

UniverSC Version 1.1.1

20 May, 2021

• update paths in documentation

• bug fixes for 10x per cell data for auto chemistry

• bug fixes for custom technology input without exiting setup

• bug fixes for short barcode whitelist with low fraction of reads

UniverSC Version 1.1.0

12 May, 2021

• add support for new technologies:

  • 5′ scRNA technologies (e.g., Smart-Seq3, ICELL8 5′ , STRT-Seq)
  • full support for combinatorial indexing (e.g., BD Rhapsody, Microwell-Seq, SCI-RNA-Seq, SPLiT-Seq, SureCell/ddSEQ)
  • full support for dual indexes (e.g., Fluidigm C1, ICELL8 full-length, inDrops v3, SCI-RNA-Seq, Smart-Seq3)
  • non-UMI technologies (e.g., ICELL8-v2, Quartz-Seq, RamDA-Seq, Smart-Seq2, STRT-Seq)

• add support for barcodes longer than 16 bp

• compatilibility with counting reads for non-UMI technologies

  • generates a mock UMI for non-UMI technologies
  • implements an option to replace UMI with mock UMI to force counting reads only

• support custom whitelists from mixed samples with a low fraction of reads

• update test cases for renaming files and compressed inputs

• bug fixes for computing summary statistics

• addresses peer-review comments

UniverSC Version 1.0.3

3 February, 2021

• unit tests for inDrops v3, SCI-Seq, Smart-Seq3

• implements support for full-length scRNA and dual indexes

• improved handling of input files and automated file detection

• automated testing with GitHub Actions

• version for submission to peer-review

UniverSC Version 1.0.2

21 January, 2021

• unit tests for 10x, dropseq, and icell8

• renaming tool and script

• version for public release