Write Consolidated AbXtract Dataset

A cube that takes processed SANGER and Quantifies Liabilities

Main Parameters

Parameter Name

Biophysical Conversion

Clustering Type

Keep Only Functional Sequences, Sanger

Max Distance for Levenshtein or Hamming, If Selected

Minimum Number of Points to Consider a Cluster

Indicate whether the ABSCAN should utilize OPTICS (preferred) or DBSCAN

Region of Interest For Clustering Sanger Sequences (Uses Clustering Type Parameter)

Write the Quick Sanger Output to CSV File

Calculation Parameters

  • Biophysical Conversion (biophysical_conversion) type: boolean: Should we convert each AA sequence into physicochemical equivalent, e.g. E,D - negative charge. This is only applicable to AbScan.
    Default: False
  • Clustering Type (cluster_type) type: string: Cluster type to apply to sequencing dataset
    Default: Unique Only
    Choices: AbScan, Unique Only, Levenshtein Distance, Hamming Distance
  • CPUs (cpu_count) type: integer: The number of CPUs to run this cube with
    Default: 1 , Min: 1, Max: 128
  • Cube Metrics (cube_metrics) type: string: Set of metrics to be collected

    Choices: cpu, disk, memory, network
  • Temporary Disk Space (MiB) (disk_space) type: decimal: The minimum amount of disk space in MiB (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 5120.0 , Min: 128.0, Max: 8589934592
  • Keep Only Functional Sequences, Sanger (filter_functional) type: boolean: Eliminates non-functional sequences, truncations, stop-codons, frame-shifts.
    Default: False
  • GPUs (gpu_count) type: integer: The number of GPUs to run this cube with
    Default: 0 , Max: 16
  • Instance Tags (instance_tags) type: string: Only run on machines with matching tags (comma separated)
    Default: “”
  • Instance Type (instance_type) type: string: The type of instance that this cube needs to be run on
  • liability database file (liabilities_db) type: file_in: Provide liabilities file (xls, csv, tsv) with 2 columns (regex pattern, name of liability)
  • Biophysical Liabilities (liability_choices_charge) type: string: Net charge or hydropathy liabilities to quantify
    Default: [‘Charge (>1)’]
    Choices: Charge (>-1), Charge (>0), Charge (>1), Charge (>2), Charge (>3), Charge (>4), Parker Hydropathy (<0.0), Parker Hydropathy (<-0.1), Parker Hydropathy (<-0.2), Parker Hydropathy (<-0.3), Parker Hydropathy (<-0.4), Parker Hydropathy (<-0.5), Parker Hydropathy (<-0.6), Parker Hydropathy (<-0.7), Parker Hydropathy (<-0.8), Parker Hydropathy (<-0.9), Parker Hydropathy (<-1.0), Parker Hydropathy (<-2.0), Parker Hydropathy (<-3.0), Parker Hydropathy (<-4.0), Parker Hydropathy (<-5.0)
  • Cysteine Liabilities (liability_choices_cysteine) type: string: cysteine-based liabilities to quantify
    Default: [‘Unpaired Cysteine’]
    Choices: Unpaired Cysteine, Any Cysteine
  • Deamidation Liabilities (liability_choices_deam) type: string: deamidation liabilities to quantify
    Default: [‘NG - Deamidation’, ‘NS - Deamidation’, ‘NT - Deamidation’, ‘NN - Deamidation’, ‘GNF - Deamidation’, ‘GNY - Deamidation’, ‘GNT - Deamidation’, ‘GNG - Deamidation’, ‘QG - Glutamine Deamidation’]
    Choices: N[GSTN] - Deamidation, NG - Deamidation, NS - Deamidation, NT - Deamidation, NN - Deamidation, GN[FYTG] - Deamidation, GNF - Deamidation, GNY - Deamidation, GNT - Deamidation, GNG - Deamidation, QG - Glutamine Deamidation
  • Glycosylation Liabilities (liability_choices_glyc) type: string: glycosylation liabilities to quantify
    Default: [‘NXT/S - Glycosylation’]
    Choices: NXT/S - Glycosylation, NXT - Glycosylation, NXS - Glycosylation
  • Hydrolysis Liabilities (liability_choices_hydrolysis) type: string: hydrolysis liabilities to quantify
    Default: [‘DP - Hydrolysis’]
    Choices: DP - Hydrolysis
  • Isomerization Liabilities (liability_choices_iso) type: string: isomerization liabilities to quantify
    Default: [‘DG - Isomerization’, ‘DS - Isomerization’, ‘DD - Isomerization’]
    Choices: D[GSD] - Isomerization, DG - Isomerization, DS - Isomerization, DD - Isomerization
  • Polyspecificity Liabilities (liability_choices_poly) type: string: polyspecificity liabilities to quantify
    Default: [‘Three Consecutive Aromatics - Polyspecificity’, ‘RR - Polyspecificity’, ‘VG - Polyspecificity’, ‘VV - Polyspecificity’, ‘WW - Polyspecificity’, ‘GGG - Polyspecificity’, ‘WXW - Polyspecificity’, ‘YY - Polyspecificity’]
    Choices: Three Consecutive Aromatics - Polyspecificity, RR - Polyspecificity, VG - Polyspecificity, VV - Polyspecificity, YY - Polyspecificity, WW - Polyspecificity, GGG - Polyspecificity, WXW - Polyspecificity
  • Max Distance for Levenshtein or Hamming, If Selected (max_dist_ld_hm) type: integer: Select the maximum edit distance for two sequences to belong to same cluster group (must be >= 1 to take effect). Works if Levenshtein Distance or Hamming Distance selected for Clustering Type. See Hidden Parameters for AbScan (though do not recommend Abscan for N<=200)
    Default: 0 , Max: 50
  • Memory (MiB) (memory_mb) type: decimal: The minimum amount of memory in MiBs (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 1800 , Min: 256.0, Max: 8589934592
  • Metric Period (metric_period) type: decimal: How often to sample metrics, in seconds
    Default: 60
    Choices: 1, 5, 10, 30, 60, 120, 180, 240, 300, Min: 1, Max: 300
  • Minimum Number of Points to Consider a Cluster (min_pts) type: integer: This is the minimum number of points that will be considered a cluster.
    Default: 2
  • Indicate whether the ABSCAN should utilize OPTICS (preferred) or DBSCAN (optics_or_dbscan) type: string: Default base algorithm to identify clusters in an unsupervised manner. Both methods use an automated application of the Elbow Estimation method, but OPTICS uses this as a max as opposed to preset value so more optimal for automation.
    Default: OPTICS
    Choices: OPTICS, DBSCAN
  • Region of Interest For Clustering Sanger Sequences (Uses Clustering Type Parameter) (roi) type: string: Indicate the region of interest for processing, only top representative full-length sequence will be kept. IF INPUT IS ILLUMINA WILL ONLY USE CDR3 (CHAIN_1/UPSTREAM CHAIN) CLUSTERING.
    Default: CDR3 Chain_2 (Downstream Chain)
    Choices: Merged CDRs, CDR3 Chain_1 (Upstream Chain), CDR3 Chain_2 (Downstream Chain), HCDR3 and LCDR3, Full-Length
  • Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to address
    Default: 64
  • Spot policy (spot_policy) type: string: Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • Write the Quick Sanger Output to CSV File (write_to_csv_file) type: boolean: Allows the option to write to CSV after the AbXtract Processing, NGS Only file at the cost of additional time. If not, can do this in separate step. Writes to empty file if turned off.
    Default: True

Hardware Parameters

Machine hardware requirements
  • Memory (MiB) (memory_mb) type: decimal: The minimum amount of memory in MiBs (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 1800 , Min: 256.0, Max: 8589934592
  • Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to address
    Default: 64
  • Temporary Disk Space (MiB) (disk_space) type: decimal: The minimum amount of disk space in MiB (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 5120.0 , Min: 128.0, Max: 8589934592
  • GPUs (gpu_count) type: integer: The number of GPUs to run this cube with
    Default: 0 , Max: 16
  • CPUs (cpu_count) type: integer: The number of CPUs to run this cube with
    Default: 1 , Min: 1, Max: 128
  • Instance Type (instance_type) type: string: The type of instance that this cube needs to be run on
  • Spot policy (spot_policy) type: string: Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • Instance Tags (instance_tags) type: string: Only run on machines with matching tags (comma separated)
    Default: “”

Metrics Parameters

Cube Metric Parameters
  • Metric Period (None) type: decimal: How often to sample metrics, in seconds
    Default: 60
    Choices: 1, 5, 10, 30, 60, 120, 180, 240, 300, Min: 1, Max: 300
  • Cube Metrics (None) type: string: Set of metrics to be collected

    Choices: cpu, disk, memory, network