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SCARF

SCARF (Scaffolded and Corrected Assembly of Roche 454) is a next-gen sequence assembly tool for evolutionary genomics designed especially for assembling 454 EST sequences against high quality reference sequences from related species.

Quick Start

  • To use SCARF, upload your data in FASTA and (optionally) 454 quality formats.
  • SCARF is presented in two implementations: SCARF and SCARF+Reference. If you are using SCARF, you must upload your own reference assembly FASTA file, while SCARF+Reference allows you to choose from the list of genomes supported by the current release of iPlant Genome Services.
  • Resources: http://barkerlab.net/software.htm

Test Data

All files are located in the Community Data directory of the iPlant Discovery Environment at the following path:

Community Data > iplantcollaborative > example_data > SCARF

To test SCARF with an user-uploaded reference sequence:

Input File(s)

  1. Use reference.fasta as the "Reference sequence file (FASTA)"
  2. Use 454.fasta as the "454 FASTA sequence file"
  3. Use 454.qual as "454 qualities file (optional)"

Parameters Used in App

When the app is run in the Discovery Environment with the above input files, leave all parameters in their default state to get the output provided in the next section below.

Output Files

Expect two output files: A .scarf file, which contains the EST assemblies, and a *scarf.info file which contains summary information about the assembly. The result files from the SCARF test case are *454.fasta.scarf and 454.fasta.scarf.info

Tool Source for App

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docs:_DE_archived_apps_blurb
docs:_DE_archived_apps_blurb