TraCeR v0.6.0

Various bug fixes.

Addition of Docker container.

New ability to recover TCR sequences from short (<50 bp) reads thanks to work from the Trinity team.

TraCeR v0.5.1

Fixes parsing of IgBLAST output from newer versions.

TraCeR v0.5.0

A new build option has been added to TraCer. This allows the user to create their own combinatorial recombinomes for new species, beyond the currently supported Mouse and Human.

Some other new features:

• Salmon is now an option for alignment
• Gamma / Delta T-Cells are supported
• Various bug-fixes and enhancements

Important: the 'kallisto_transcriptome' option in the tracer config must be changed to 'base_transcriptome' due to the added support of salmon

TraCeR v.0.4.0

IMPORTANT: Python dependencies have changed since the last release. Use the requirements file (detailed here) to update them if necessary.

This release contains code changes to improve future development along with the additions and fixes below:

• Compatibility for Trinity v2 as well as v1
• Option to skip plotting network graphs. Useful if graphviz isn't working
• Option to pass graph_format to test
• Improved installation of Python dependencies
• Code reformatting
• Python 3 compatibility
• Started to add unit tests
• Bug fixes

TraCeR v0.3.0

This release contains a way to test your installation and setup, improved output files from summarise and bug fixes.

Test data

A new tracer test function (see README for details) runs all the steps of assemble and summarise using a small test data set. This will help to check whether all of the prerequisites are working and if config file is correct.

Summarise output

The summarise output now includes the following:

1. A recombinants.txt file that details the recombinants that were reconstructed in each cell.
2. Text files containing the underlying data for the reconstructed lengths and clonotype size graphs.
3. Labelled axes on the reconstructed lengths and clonotype size graphs.

TraCeR v0.2.3

Bug fixes including fix for change in the way NetworkX behaves for writing .dot files.

TraCeR v0.2.2

Small fix to improve IgBlast command and improve Readme instructions for install IgBlast

TraCeR v0.2.1

Fixed filename mismatch in Human Igblast DB files that was preventing assessment of human sequences.

TraCeR v0.2.0

• Added ability to use single-end sequencing data
• Added --seq_method option for assessment of recombinant productivity
• Bug fixes

TraCeR v0.1.2

Based on user feedback made a small change to the Readme to emphasise that base transcriptome files should be unzipped.