The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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Rationale and background: 

 

DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high-performance analysis of big sequence data. The key features are: 

  • Pairwise alignment of proteins and translated DNA at 500x-20,000x speed of BLAST.
  • Frameshift alignments for long read analysis.
  • Low resource requirements and suitable for running on standard desktops or laptops.
  • Various output formats, including BLAST pairwise, tabular and XML, as well as taxonomic classification.

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The test data are provided for testing DIAMOND-makedb-0.9.10 is in here - /iplant/home/shared/iplantcollaborative/example_data/diamond_blast:

Use the following inputs/outputs for testing DIAMOND-makedb-0.9.10

  1. Mandatory argument

    1. Input file - sample.faa

    2. Database file - out (Default)

Output Reports:

  1. out.dmnd - Final database for the input file (sample.faa). 

    Now you can proceed to actual DIAMOND Blast

 

More information about DIAMOND-makedb-0.9.10 can be found at https://github.com/bbuchfink/diamond

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