Release Notes

v0.1.9 July 2024

A bug has been fixed in both the Quick Sanger from ABI Traces - AbXtract Floe and the Quick Sanger from DNA or Amino Acid Sequence Files – AbXtract Floe. The sequence_issue column was missing a detailed breakdown of frameshifts by region. This also affected filtering out of frame shifted sequences when the Floe’s filter_functional toggle was set to On. It has been restored.
A bug has been fixed in the Quick Sanger from ABI Traces - AbXtract, Quick Sanger from DNA or Amino Acid Sequence Files – AbXtract, and NGS Pipeline - AbXtract Floes. The multi-selection of species from the database was resulting in run failures but has now been fixed.

New release includes a new floe built for faster and less computationally intensive processing of NGS data. This flow is called NGS Pipeline Efficiency - AbXtract. It allows the user to only print a subset of the failed records, reducing the run time of this cube.
New misannotation detection and classification for both functional and non-functional sequences in Quick Sanger floes.
Update to Quick Sanger from ABI Traces floe to allow user to enter multiple forward and reverse primer names.
Minor Update: Upstream floe report stratifies general stats table by barcode group and is transposed to improve readability.
Minor Update: Downstream floe report provides stats for ALL clusters in the general stats table per barcode group before being subsetted to only the top 100 clusters for plotting.

New release to include new clone tracer floe called Multiple Round Relative Abundance and Enrichment Calculation by Region of Interest (ROI)
First release of Quick Sanger from ABI Traces - AbXtract, which can now process ABI Traces.
Major update that drastically improves the speed of liability processing using the Liability Quantification Across CDRs floe.
Major update that can now process compressed FASTQ.GZ files in all NGS processing floes without need for any decompression, drastically reducing storage overhead and upload times.
Major update to Floe Reports, particularly key selection outputs in the automated floes, allowing visualization of selected clones in the context of clusters.
Major improvement to the floe Quick Sanger from DNA or Amino Acid Sequence Files, to improve the reporting on sequencing errors.
Minor update to enable one to skip consolidation in Quick Sanger, whereby all input clones correspond to output.
Minor update to track all clones in Quick Sanger, including those that do not pass annotation, with error reporting. Additional options to skip consolidation of Sanger sequences, such that number of rows in a dataset corresponds to number of input clones, or consolidate by subpopulation as defined in the clone name.

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

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.

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.

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".