Release Notes

v0.1.4 December 2022

  • Major update to enable sequence error correction through processing of unique molecular identifiers prior to sequence annotation.

v0.1.3 June 2022

  • Minor bugfix to edit distance functionality to take on a more greedy approach when clonotyping sequences.

  • Minor fix to NGS Pipeline that changes the default region of interest (ROI) to HCDR3 and LCDR3, as recent data suggests this is more important ranking parameter relative to HCDR3 only.

  • Major update to enable conversion of AIRR-compatible TSV/CSV/XLS/XLSX files to AbXtract-compatible datasets.

  • Major update to enable export of AbXtract-compatible datasets to AIRR-compatible CSV files.

  • Update to add basic clonotyping (Levenshtein and Hamming distance) to Quick Sanger cube. AbScan functionality added as well, but typically due to the sample size, would not recommend using on Sanger datasets.

  • Update to tabulate sequence-based metrics important to viscosity / stability of antibodies including N_philic, N_phobic, isoelectric point, charge_symmetric_parameter, high_viscosity_index as reported in Lai et al (Trout Lab), 2021 Molecular Pharmaceutics. These are included in Quick Sanger and NGS Pipeline Floes.

  • Added count_fl_early, count_fl_final, count_fl, percent_fl_early, percent_fl_final, percent_fl to gain a default understanding of the original count and percent in source population.

  • Added ratio_to_top_early, ratio_to_top_final, ratio_to_top_early_final to understand how well the 2nd, 3rd, 4th clone in cluster compares to top clone in terms of relative frequency.

v0.1.2 April 2022

  • Minor bugfix to Automated Top Lead Selection - AbXtract floe to improve output in event number of clusters is below desired.

  • Minor bugfix to Consolidate Cube - fixes issue to check that record has value, which caused some errors if header not appropriately identified.

  • Minor bugfix to IgMatcher cube that increases the default min votes from 100 to 150. This increases the stringency of germline/scaffold assignment.

  • Minor update add fields noise_cluster_1 and noise_cluster_2 to differentiate unsupervised cluster from assignment.

v0.1.1 March 2022

  • Minor bugfix of plotly includes for floe reports

v0.1.0 December 2021

General Notice

  • This is the initial release of the AbXtract module

  • This package is built using openeye-orionplatform==4.0.0 and "OpenEye-Snowball==0.21.3".