BRILIAv3.5.7beta

See Patch for more details.

Still in testing - full characterization of annotation accuracy is not completed yet.

• Reworked the B-cell phylogeny algorithm
• Reworked inputs to BRILIA
• Set an incomplete annotation to those with CDR3 lengths <5 or >30 amino acid long, or with >15 nt deletions of V, D, or J gene edges
• Added more command-line features to search and process files
• Added fastq file alignment quality filters (MinQuality), which will set low-quality base read as wildcard "N"
• Added ability to use custom VDJ gene databases if fasta files are provided
• Added and fixed post-processing code (mergeSimilarSeq) to remove sequences that diff less than a Cutoff hamming distance (integer >= 1) or fraction (between 0 and 1).
• Added BRILIA test functions

PERFORMANCE IMPROVEMENTS

• Moved more function to C++ for speed enhancement
• Made annotation and plotting codes multi-threaded
• Added parallel computing progress tracker (ProgressTracker.m)

BRILIAv3.1.5

• Fixed a bug with runAnalysis.m in v3.1.5
• This one will automatically move sequences into the Err.csv file that have poor V/J annotations with > 40% hamming distance mismatch. This is usually caused by short RNA sequences that are not a VDJ junction.
• Can now input file names that have a space in them by using quotes.
  EX: BRILIA.exe "C:\Temp Dir\SeqData.csv" Species Mouse Chain H

BRILIAv3.1.3

• ~4x faster performance than v3.0.x due to MEX (C++) codes.
• Can run BRILIA in its own environment via
  Windows: BRILIA.exe
  Linux: run_BRILIA.sh [mcr_path]
• Added Zebrafish to the species list

BRILIAv3.0.14

• Fixed some critical infinite loop issues with plotTree features.
• Prevents parallel processing from shutting down prematurely.
• Some general security fixes.
• Fixed issues with ambiguous character nt to aa translations.
• Enable annotation-only capabilities via the 'AnnotOnly y' setting.

BRILIAv2.0.7

BRILIAv2.0.7.zip

This version has the first GUI for BRILIA. Should be able to process simple sequence files and plot lineage trees per cluster. Includes better examples of input files with template count / copy count information.