OE Sanger Assembly

A cube that prepares ab1 files from Sanger sequencing for annotation

Main Parameters

Parameter Name

Check for multiple clones in well

Name of forward primer

Input ab1 files

Parameter Details

Calculation Parameters

  • Check for multiple clones in well (check_poly) type: boolean: Checks for overlapping traces in Chain 2 CDR3 as indicator of multiple clones. Checks average quality score of CDR3 compared to FR3 and flags clones falling below…
    Default: False
  • 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
  • Name of forward primer (for_primer_name) type: string: Used to parse forward reads from ab1 files by name. Primer should be the last part of the file name.
    Default: “”
  • GPUs (gpu_count) type: integer: The number of GPUs to run this cube with
    Default: 0 , Max: 16
  • Input ab1 files (input_ab1_forward) type: file_in: Can accept multiple (paired and/or repeat) reads per clone. Base calls in assembly are determined by majority vote at each position.
  • 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
  • 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
  • Downstream sequence mismatches (mismatches_down) type: integer: Number of substitutions to allow in downstream sequence match.
    Default: 0
  • Upstream sequence mismatches (mismatches_up) type: integer: Number of substitutions to allow in upstream sequence match.
    Default: 0
  • Name of reverse primer (rev_primer_name) type: string: Used to parse reverse reads from ab1 files by name. Primer should be the last part of the file name.
    Default: “”
  • 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
  • Trim nucleotides downstream of this sequence (trim_bases_down) type: string: Trim nucleotides downstream of this sequence to remove primer and/or extraneous sequence prior to annotation. Identifies last instance of this sequence.
    Default: “”
  • Trim nucleotides upstream of this sequence (trim_bases_up) type: string: Trim nucleotides upstream of this sequence to remove primer and/or extraneous sequence prior to annotation. Identifies first instance of this sequence.
    Default: “”
  • Trim # nucleotides downstream of this sequence (trim_length_down) type: integer: Trim # nucleotides downstream of this sequence to remove primer and/or extraneous sequence prior to annotation.
    Default: 0
  • Trim # nucleotides upstream of this sequence (trim_length_up) type: integer: Trim # nucleotides upstream of this sequence to remove primer and/or extraneous sequence prior to annotation.
    Default: 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