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This page lists all current tutorials for all platforms.

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App/Workflow NameAuthorCreatedUpdatedPlatformTypeAreaGoalApps UsedMajor Steps (do we need this?)
Evaluate and Pre-Process Sequencing ReadsBarthelson6/12/14


DEWorkflowRead cleanupClean and filter Illumina reads using DE apps.
  1. FastQC 0.10.1 (multi-file)
  2. Scythe-adapter-trimming
  3. Sickle-quality-based-trimming
  4. Prinseq-Graph-noPCA evaluate reads

Evaluate read quality, Remove adapter sequences, Filter sequences by quality, Reevaluate read-quality of the cleaned reads, Use an alternative method to evaluate read-quality

BLAST a TranscriptomeHilgert7/21/147/21/15DEWorkflow 

Become familiar with a procedure to reduce the number of transcripts and the level of redundancy in an assembled transcriptome, and to identify coding sequences that can be submitted to BLASTP searches.

  1. Select contigs
  2. CD-HIT-est 4.6.1
  3. Transcript decoder 1.0
  4. Blastp-2.2.29
    OR: DeltaBLAST-2.2.29

Eliminate small transcripts, Reduce transcript redundancy, Identify and translate coding sequences, Submit translated transcriptome to BLASTP OR: Submit translated transcriptome to Delta-BLAST

Assemble a Genome Using SOAPdenovo


Gain familiarity with a commonly used procedure for de novo whole genome assembly of Illumina reads using the DE. Includes assembly of paired and unpaired Illumina reads with SOAPdenovo2, followed by an analysis of the assembly quality.

  1. SOAPdenovo 2.0.4
  2. Assess assembly vs whole genome

Assemble reads, Assess assembly

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