TRUST4 v1.0.10

• Add the option "--readFormat" that simplifies the read/barcode specification syntax.
• Add the option "--barcodeTranslate" to translate barcodes to another set of strings, and this option supports subset translation.
• Fix several issues in the perl script regarding creating IMGT sequence (Thanks to @Rudolph-afk )

TRUST4 v1.0.9

• Remove the limitation of read length (10000bp before).
• Add the script to add IMGT gaps to the AIRR output.
• Expose the assembly k-mer and minimum hit length option to the user.
• Cleaner secondary chains in the barcode report file.
• Allow assembly stage to use --ref file. This is for the case that the gene names in -f reference file is not starting with TR{BAGD} or IG{HKL}.

TRUST4 v1.0.8

• Use barcode count for the trust_report.tsv file when using "--barcode" option. This allows TRUST4 to work seamlessly with UMI-based TCR-seq/BCR-seq data through the option "--barcode-level molecule".
• Fix a bug of reporting partial CDR3 as complete in rare cases
• Fix several bugs in AIRR format

TRUST4 v1.0.8-beta

• Output the sequence_alignment and germline_alignment fields in the AIRR format. Now TRUST4 outputs all the required fields in the AIRR format.
• Output the AIRR file for the SMART-seq-like data.
• Supporting barcodes at the molecular level
• The secondary chain fields in the barcode_report file contain all types of chains. We also added the script "barcoderep-expand.py" to expand each barcode to represent those secondary chains for the case where each barcode contains multiple cells.
• Improve the speed of processing BAM input.

TRUST4 v1.0.7

• Fix an issue of abundance estimation
• Fix an issue of throwing "Unkown parameters", e.g: #74, #98
• Use the report file to drive the AIRR output
• Fix other small bugs

TRUST4 v1.0.6

• Output files in the AIRR format.
• Fix an issue of provided mouse reference genome sequences.
• Provide a script to remove possibly leaked CDR3 sequences in barcode file.
• Add the option to output more than one pair of chains in the smart-seq wrapper.
• Other small bugs fixed.

TRUST4 v1.0.5.1

• Output read count in the abundance column in trust-stats.py
• Fix a serious bug in the run-trust4 wrapper in the original v1.0.5 release for single-cell data.

TRUST4 v1.0.5

• Add the option "--needReverseComplement" and "--fastq" to annotator so it can handle raw unstranded data
• Add the option "--outputReadAssignment" where the read assignment will be output to {prefix}_assign.out file
• Add the option '--imputeBCR" to trust-barcoderep.pl so BCR CDR3 information can also be imputed when specified
• Fix a small issue in extracting candidate reads with respect to tandem repeats
• Fix several bugs

TRUST4 v1.0.4

• Add the script trust-stats.py to summarize immune repertoire statistics for each report or barcode-report file
• Fix an issue in scaffolding, which may cause wrong abundance estimation
• Fix several bugs

TRUST4 v1.0.2

• Add a column to specify whether the corresponding assembled contig is full-length
• Improve the sensitivity of annotating full-length assemblies.
• Fix a bug of wrongly filtering "TRAV/DV" genes in IMGT annotation file. (Thanks to @danich4114)
• Fix other small bugs