rust-mdbg 0.1.0 magic-simplify

Owned by Amanda Cooksey (Unlicensed)
Sept 23, 2021
1 min read

Quick Start

To use rust-mdbg 0.1.0 magic-simplify, import your output data from rust-mdbg 0.1.0

rust-mdbg is a modular assembler. It consists of three components:

  1. rust-mdbg, to perform assembly in minimizer-space
  2. gfatools (external component), to perform graph simplifications
  3. to_basespace, to convert a minimizer-space assembly to base-space
    (For convenience, components 2 and 3 are wrapped into a script called magic_simplify.)

For better contiguity, try the provided multi-k assembly script. It performs assembly iteratively, starting with k= 10, up to an automatically-determined largest k. This comes at the expense of ~7x longer running time.

There are 4 rust-mdbg apps in the DE:

  1. rust-mdbg 0.1.0
  2. rust-mdbg 0.1.0 magic simplify
  3. rust-mdbg 0.1.0 pipeline (runs both apps 1 and 2)
  4. rust-mdbg 0.1.0 multik

Test Data

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> rust-mdbg

Input File(s)

Use the following files from the directory above as test input.

  • example.140310728378112.sequences
  • example.140310730479360.sequences
  • example.140310732580608.sequences
  • example.140310734681856.sequences
  • example.140310736783104.sequences
  • example.140310738884352.sequences
  • example.140310740985600.sequences
  • example.140310743086848.sequences
  • example.gfa

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

  • Use these parameters within the DE app interface:
    • Specify the prefix of the input files (output from rust-mdbg 0.1.0)

Output File(s)

Expect the following as output.

  • example.140566115636992.sequences
  • example.140566117738240.sequences
  • example.140566119851776.sequences
  • example.140566121965312.sequences
  • example.140566124078848.sequences
  • example.140566126204672.sequences
  • example.140566128305920.sequences
  • example.140566130407168.sequences
  • example.gfa
  • example.msimpl.fa
  • example.msimpl.gfa

Tool Source for App