WF_0_Assembler.md

Workflow 0 Script

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Prepares raw reads and assembles genome

WF_0_Assembler_runner.py

• run_assembly()
  • Calls run_assembler, sample_organizer, data_pre_processor, and check_assembly_qual from helper file
  • Returns list of sample id's and assembly metrics

WF_0_Assembler_helper.py

• sample_organizer()

  • Function finds reads and organizes them into a dict
  • Returns Dictionary of all{SampleID: [R1,R2]}

• data_pre_processor()

  • Removes low quality reads and trimmes reads
  • Returns {SampleID: [R1,R2]}} for new fastq files

• run_assembler()

  • Runs Spades assembly