Clustering by AbScan, Edit Distance, or 100% Homology

Takes in set of records and will cluster the region of interest (roi) using unsupervised clustering or other standard cluster approaches such as condensing by unique sequences only, Levenshtein distance or hamming distance. The output will be a set of sequences that have a cluster assigned to it based on the roi.

Main Parameters

Parameter Name

Biophysical Conversion

Clustering Type

Keep Only Functional Sequences

Max Distance for Levenshtein or Hamming, If Selected

Minimum Number of Points to Define a Cluster

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

Region of Interest For Clustering

Minimum Count for the Region of Interest (ROI)

Minimum Percent for the Region of Interest (ROI)

Write the AbScan Output to CSV File

Xi Minimum Steepness of Reachability Plot

Parameter Details

Calculation Parameters

  • Biophysical Conversion (biophysical_conversion) type: boolean: Convert sequences to physicochemical equivalent, e.g. E,D - negative charge. This is only applicable to AbScan and does not apply to Unique Only, Levenshstein distance or Hamming distance
    Default: True
  • Clustering Type (cluster_type) type: string: Cluster type to apply to sequencing dataset
    Default: AbScan
    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 (filter_functional) type: boolean: Eliminates non-functional sequences, truncations, stop-codons, frame-shifts
    Default: True
  • 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
  • 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.
    Default: 2 , 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 Define 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 (roi) type: string: Indicate the region of interest (ROI) for processing. If Illumina, will only use upstream ‘cdr3_aa_1’ for clustering for AbScan, Levenshtein and Hamming. If option ‘Unique Only’ with Illumina, will condense according specified ROI according to chain_1.
    Default: CDR3 Chain_2 (Downstream Chain)
    Choices: Merged CDRs, CDR3 Chain_1 (Upstream Chain), CDR3 Chain_2 (Downstream Chain), HCDR3 and LCDR3, Full-Length
  • Minimum Count for the Region of Interest (ROI) (roi_count) type: integer: This will set the minimum count for a given region of interest, all below will be removed.
    Default: 1 , Min: 1, Max: 10000000000
  • Minimum Percent for the Region of Interest (ROI) (roi_percent) type: decimal: This will set the minimum percent for a given region of interest, all below will be removed.
    Default: 1e-12 , Min: 1e-12, Max: 100
  • 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 AbScan Output to CSV File (write_to_csv_file) type: boolean: Allows the option to write to CSV after the AbXtract Processing at the cost of additional time. If not, can do this in separate step.
    Default: True
  • Xi Minimum Steepness of Reachability Plot (xi) type: decimal: Float value between 0 and 1. Value sets the minimum steepness on the reachability plot to define cluster boundary. An upwards
point in reachability is essentially the ratio from one point to successor being at most 1-xi.
Default: 0.0 , Max: 1.0

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