1.3.1

Update VDJtools

1.2.2

License upd

1.2.1

jitpack tag

VDJmatch algorithm

Implemented TCR similarity metric and smart algorithms for VDJdb querying.

Java 9 compatibility

• Now should work with Java 9
• Other minor fixes

N.B Please ignore An illegal reflective access operation has occurred warnings occurring when running with Java 9, they have no effect on software performance/output whatsoever

Server compatibility release

1.1.6

Upd sh script

Better summary stats

Minor fixes, update VDJtools version, better annotation summary output

Cleanup release

Removed some experimental functions & fixed sever bugs

Scoring update

Critical fix for scoring system:

• Re-named and modified presets: hamming (hamming distance based); 5,2,2,7 search scope followed by high-recall (precision corresponding to recall of 80%), optimal (precision and recall corresponding to highest F1 measure)
• Scoring selection by precision and recall (selects nearest pre-trained preset matching specified value)
• Ensure that exact matches are always reported disregarding score threshold

Scoring & VDJtools compatibility

Major improvements:

• VDJtools compatibility. Now output of VDJdb annotation can be used for downstream analysis with VDJtools and vice-versa. See README for additional info.
• New scoring scheme: search is performed by first looking up candidate CDR3 sequences with a high number (up to 7) mismatches allowed. The resulting alignments are scored based on substitution matrix and gap scores optimized for precision and recall by running NSGAII for VDJdb alignments (see README). While that slows down VDJdb, we take advantage of suffix tree search that automatically generates alignments and the effect is not that dramatic.

Minor improvements:

• Support all software input formats that are supported by VDJtools
• Some refactoring that should speed-up scored search
• Completely re-wrtitten summary report generation
  • More intuitive summary table
  • Compatibility for sunburst charts in VDJdb-server

Bug fixes:

• Disabled annotation for non-coding clonotypes

Note:

• Search and VDJdb confidence threshold parameters are optimized for latest VDJdb assembly