OE Sanger Read Pairing

A cube that pares ab1 files from Sanger sequencing for assembly

Main Parameters

Parameter Name

Input files

Parameter Details

Calculation Parameters

  • 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 (read 1) from ab1 files by name. Primer should be the last part of the file name, e.g., Clone1-PrimerF.ab1. Click the + to add additional forward primer names. Recommended: include the delimiter (e.g., ‘-’) preceding the primer name to ensure it is removed from the clone ID in the output dataset.
    Default: []
  • GPUs (gpu_count) type: integer: The number of GPUs to run this cube with
    Default: 0 , Max: 16
  • Input files (input_ab1_forward) type: file_in: Provide either one or more individual ab1 files, or a zip archive comprised of one or more folders of ab1 files. Accepts paired or single-directional reads. A primer name must be part of the ab1 file names. In the case of repeat sequencing, all repeat traces can be provided. The reads with highest average quality will be used in assembly. NOTE: .zip files can be uploaded to Orion using the ‘+Add Data’ option, but you must click ‘Show advanced options’ and set ‘Processing method’ to ‘None’ prior to clicking ‘Upload’.
  • 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
  • Read pre-filtering minimum length (pre_filter_min_len) type: integer: Reads below this length will be flagged.
    Default: 400
  • Read pre-filtering minimum average quality (pre_filter_min_qual) type: decimal: Reads below this average quality will be flagged.
    Default: 40.0
  • Name of reverse primer (rev_primer_name) type: string: Used to parse reverse reads (read 2) from ab1 files by name. Primer should be the last part of the file name, e.g., Clone1-PrimerR.ab1.Click the + to add additional reverse primer names. Recommended: include the delimiter (e.g., ‘-’) preceding the primer name to ensure it is removed from the clone ID in the output dataset.
    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

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