OE Sanger Assembly P

A cube that prepares ab1 files from Sanger sequencing for annotation

Main Parameters

Parameter Name

Check for multiple transformants

Which Sanger trace covers the heavy chain?

Trim left read 1

Trim left read 2

Trim right read 1

Trim right read 2

Read trimming stringency

Related Cubes

Parameter Details

Calculation Parameters

  • Check for multiple transformants (check_poly) type: boolean: Checks for overlapping traces in Chain 2 CDR3 as indicator of multiple transformants. Checks average quality score of CDR3 compared to last 12nt of FR3 and flags clones where average quality over CDR3 < 0.5x average quality of last 12nt of FR3. Multiple transformants flag will appear in sequence_issue column of output dataset. This method only works when sequencing includes these two regions.
    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
  • GPUs (gpu_count) type: integer: The number of GPUs to run this cube with
    Default: 0 , Max: 16
  • Which Sanger trace covers the heavy chain? (heavy_chain_read) type: string: To be used when check_poly=True. Indicate whether heavy chain CDR3 is primarily covered by the forward trace or reverse trace (i.e., are the chains oriented VL-VH, in which case choose reverse, or are they oriented VH-VL, in which case choose forward.
    Default: reverse
    Choices: forward, reverse
  • 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: 1
  • Upstream sequence mismatches (mismatches_up) type: integer: Number of substitutions to allow in upstream sequence match.
    Default: 1
  • 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 after assembly and 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 after assembly and prior to annotation. Identifies first instance of this sequence.
    Default: “”
  • Trim left read 1 (trim_left1) type: integer: Number of bases to trim from left end of read 1 (forward read) prior to assembly. Will only be applied if Read Trimming Stringency is set to 0.
    Default: 50
  • Trim left read 2 (trim_left2) type: integer: Number of bases to trim from left end of read 2 (reverse read) prior to assembly. Will only be applied if Read Trimming Stringency is set to 0.
    Default: 50
  • Trim # nucleotides from 5-prime end of read (trim_length_down) type: integer: Trim # nucleotides from 5- end of assembled read to remove primer and/or extraneous sequence prior to annotation.
    Default: 0
  • Trim # nucleotides from 3-prime end of read (trim_length_up) type: integer: Trim # nucleotides from 3-prime end of assembled read to remove primer and/or extraneous sequence prior to annotation.
    Default: 0
  • Trim right read 1 (trim_right1) type: integer: Number of bases to trim from right end of read 1 (forward read) prior to assembly. Will only be applied if Read Trimming Stringency is set to 0.
    Default: 50
  • Trim right read 2 (trim_right2) type: integer: Number of bases to trim from right end of read 2 (reverse read) prior to assembly. Will only be applied if Read Trimming Stringency is set to 0.
    Default: 50
  • Read trimming stringency (trim_stringency) type: integer: Stringency of read trimming prior to assembly. If value is 0, floe ignores this parameter and trims by length (see ASSEMBLE TRACES Cube hidden parameters to set lengths).To enable this parameter, choose an integer between 1-9. 1 is the most stringent and 9 is the least stringent. Incompletely trimmed reads may result in insertions in the assembled sequence but too much trimming may remove clone start and end sites.
    Default: 5

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

Parallel Sanger Assembly

The parallel version adds these extra parameters.

  • Number of messages to distribute at a time (item_count) type: integer: The maximum number of messages to bundle together for a parallel cube.
    Default: 1 , Min: 1, Max: 65535
  • Maximum Failures (max_failures) type: integer: The maximum number of times to attempt processing a work item
    Default: 10 , Min: 1, Max: 100
  • Autoscale this Cube (autoscale) type: boolean: If True, let Orion manage the parallelism of this Cube
    Default: True
  • Maximum number of Cubes (max_parallel) type: integer: The maximum number of concurrently running copies of this Cube
    Default: 1000 , Min: 1
  • Minimum number of Cubes (min_parallel) type: integer: The minimum number of concurrently running copies of this Cube
    Default: 0