May 24, 2022

Public workspaceERGA_AssemblyProtocol_Template

This protocol is a draft, published without a DOI.
  • ann.mccartney 1
  • 1national institute of health
ann.mccartney
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Protocol Citation: ann.mccartney 2022. ERGA_AssemblyProtocol_Template. protocols.io https://protocols.io/view/erga-assemblyprotocol-template-b9tzr6p6
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: In development
We are still developing and optimizing this protocol
Created: May 23, 2022
Last Modified: May 24, 2022
Protocol Integer ID: 63065
Keywords: erga-assemblyprotocol-template erga-assembly-strategy, sac committee
Abstract
ERGA_Assembly_Strategy

Abstract written by SAC Committee.
Guidelines
Any Guidelines Recommended by SAC
Computing Environment Used
2d

Please enter all details of the compute system your analyses was carried out on

Equipment
Name
NAME
Type
TYPE
Brand
BRAND
xxxx
SKU

Data Cleaning
2d
Please enter instructions on how your cleaned your data
  • Software
  • Summary of approach
  • Version
  • Code
  • System Requirements
  • Additional Tips for usersDuration00:00:00
Command
Data Cleaning Code Used
Commands Used


Assembly Polishing
Please enter instructions on how your assembled your long read data
  • Data Type, VolumeAmount0 Numbers of reads
  • Summary of approach
  • Assembly software, Version
Software
Software Used
NAME

  • Purging software
Software
Software Used
NAME

  • System Requirements Duration00:00:00
  • Additional Tips for users
Note


  • Code
Command
The code I used to generate my primary assembly (The system I used)
Assembly Commands Used
The Command I used




Assembly Scaffolding
2d
Please enter instructions on how your scaffolded your long read assembly
  • Data Type, Volume (before after filtration)Amount0 Numbers of reads
  • Summary of approach
  • Scaffolding software, Version
Software
Name of Software
NAME

  • System Requirements Duration00:00:00
  • Additional Tips for users
Note


  • Code

Command
Scaffolding Commands
Commands Used

Assembly Polishing
2d
Please enter instructions on how your polsihed your final assembly
  • Data Type, VolumeAmount0 Numbers of reads
  • Summary of approach
  • Polishing software, Version
Software
Software Used
NAME

  • System Requirements Duration00:00:00
  • Additional Tips for users
Note


  • Code




Command
Polishing Commands Used
Commands



Assembly QC
2d
QC
  • Please enter instructions on how your QC'd your final assembly
  • Summary of approach
  • Softwares used, Version
Software
Software Used
NAME

  • GRIT curation employed?
  • System RequirementsDuration00:00:00
  • Additional Tips for users
Note


  • Code


Command
QC Commands
Commands