Automated Top Lead Selection - AbXtract

Category Paths

  • Solution-based/Biologics/Antibody Design

  • Role-based/Bioinformatician

  • Role-based/Biologist

  • Product-based/AbXtract

Description

Automatically select the top X number of sequences across defined cluster space using rank ordered, user-specified metrics.

Promoted Parameters

Title in user interface (promoted name)

NGS Key Selection Parameters

Maximum Number of Full-Length Sequences (number_of_seqs_ngs_picking): Indicate the maximum number of full-length, non-redundant sequences. This value depends on the total number of non-redundant sequences, maximum # of clusters and the maximum # of sequences per cluster. If the total number is below desired, try adjusting max # of clusters or max number of sequences per cluster. Alternatively, if you want to fill quota with additional sequences per cluster turn on the ‘Attempt to Fulfill the Desired Number of Sequences Quota’ parameter

  • Required

  • Type: integer

  • Default: 100

Maximum Number Sequences Per Cluster (max_seq_per_cluster): Indicate the maximum number of unique full-length sequences per given cluster. This value may be exceeded if the ‘Write the Automated Top Clones Output to CSV File’ is turned ON

  • Required

  • Type: integer

  • Default: 10

Maximum Number of Clusters Preferred? (number_of_clusters_to_select_from): Indicate the maximum number of clusters that you want to choose from. This value may be exceeded if the ‘Write the Automated Top Clones Output to CSV File’ is turned ON

  • Type: integer

  • Default: 40

Metrics for Ranking (picking_choices): Place metrics in order of ranking (if nothing, ranks by full-length count)

  • Required

  • Type: string

  • 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)’]

Rank Sanger Clones First in Population (rank_sanger): Sanger clones, if present, will be ranked first.

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Attempt to Fill the Desired Number of Full-Length Sequences Quota (quota_attempt): This will attempt to fulfill the total number of sequences quota if goal of desired number of full-length sequences is not reached by 1) selecting additional clones across lower in rank aross designated clusters followed by 2) selecting the remaining top ranked clones from different clusters by prioritizing top clones. NOTE: if turned on, this is likely to result in a greater number of sequences per cluster and if quota still not met, more clusters then designated in total to reach the desired number of full-length sequences goal

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]