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GCAT-SEEK Eukaryotic Genomics Workshop Manual

Developed by Dr. Vince Buonaccorsi at Juniata College, the GCAT-SEEK Eukaryotic Genomics Workshop Manual consists of seven chapters that cover genome assembly, gene annotations, and variant calling:

  1. Genome assembly I: Quality control with FastQC and Trimmomatic
  2. Genome assembly II: Assembly size estimation and k-mer graphs
  3. Genome assembly III: Assembly algorithms
  4. Genome annotation with Maker I: Overview and repeat finding
  5. Genome annotation with Maker II: Whole genome analysis
  6. Whole genome annotation: Miscellaneous methods
  7. SNP calling and interpretation

CourseSource Publication

Buonaccorsi, V.P., Hamlin, D., Fowler, B., Sullivan, C., and Sickler, A. 2017. An Introduction to Eukaryotic Genome Analysis in Non-model Species for Undergraduates: A tutorial from the Genome Consortium for Active Teaching. CourseSource.

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GCAT-SEEK Workshop Training Materials

This collection contains the workshop manuals from previous GCAT-SEEK workshops. The topics covered in these manuals include genome assembly, eukaryotic genome annotations, metagenomics, and RNA-Seq.

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Wilson Leung