Custom SANGER Select of Additional NGS Representatives by Group - AbXtract

Category Paths

  • Solution-based/Biologics/Antibody Design

  • Role-based/Bioinformatician

  • Role-based/Biologist

  • Product-based/AbXtract

Description

This will identify all non-redundant antibodies that share the same cluster or region of interest (ROI), user-specified, as the SANGER. If an OPTIONAL Custom SEQ ID file is provided (containing seq_id in column A and max number of clones in column B) it can indicate the number of desired non-redundant clones by the given SANGER seq_id. If no custom file is provided, then the FLOE will automatically select desired number of leads for all non-redundant SANGER sequences.

Parameter title in user interface (promoted name)

  • Output CSV Filename (file_name) type: file_out: All records are written to Custom SANGER Select CSV file, must contain the *.csv extension
    Default: sanger_select.csv

Parameter title in user interface (promoted name)

  • Failed Dataset Output Name (data_out) type: dataset_out: Contains failed records from both upstream and downstream processes
    Default: problematic.custom_sanger_select

Parameter title in user interface (promoted name)

  • Remove Non-Functional or Aberrant Sequences (filter_functional) type: boolean:
    Default: True

Parameter title in user interface (promoted name)

  • Max number of unique NGS desired? (number_of_sequences_total) type: integer: Please choose the maximum number full-length unique sequences desired per clone.
If custom file input, will override this parameter.
Default: 10 , Min: 1, Max: 1000000

Parameter title in user interface (promoted name)

  • Metrics for Ranking (predict_choices) type: string: Place metrics in order of ranking (if nothing, ranks by full-length count)
    Default: [‘ROI Percent, Final Round Only’, ‘Full Length (Corrects for Illumina or PacBio), Percent’, ‘Liabilities Both Chains’, ‘Liabilities CDR3_2’]
    Choices: Full Length (Corrects for Illumina or PacBio), Count, Full Length (Corrects for Illumina or PacBio), Percent, ROI Count, Final Round Only, ROI Percent, Final Round Only, ROI Fold Enrichment, Final Round Only, ROI Log2 Enrichment, Final Round Only, Liabilities Both Chains, Liabilities Chain_2, Liabilities Chain_1, Liabilities CDR1_1, Liabilities CDR2_1, Liabilities CDR3_1, Liabilities CDR1_2, Liabilities CDR2_2, Liabilities CDR3_2, ROI Count, Early Round Only, ROI Percent, Early Round Only, Cluster Count (e.g. unique sequences per cluster), Cluster Percent (e.g. unique rep per cluster)

Parameter title in user interface (promoted name)

  • Region of Interest (ROI) to Select Top Representatives (roi) type: string: Select the cluster or region of interest (ROI) that match desired sequence ID for SANGER. IMPORTANT, if cluster is selected then all sequences should come from the dataset that was clustered at the same time
    Default: Cluster
    Choices: Cluster, Cluster_CDR3_1, Cluster_CDR3_2, Merged CDRs, CDR3 Chain_1, CDR3 Chain_2, HCDR3 and LCDR3, Full-Length

Parameter title in user interface (promoted name)

  • Output Name of the Custom Sanger Selected Population (data_out) type: dataset_out: Output dataset to write to
    Default: sanger_selected