Sequence Analysis

Learning Goals

Participants should be able to:

Time and Place

Online at the IMB Bioinformatics Slack

Session 1: Thursday 4-5pm 28.05.20 Session 2: Tuesday 4-5pm 02.06.20 Session 3: Thursday 4-5pm 04.06.20

Required Materials

See Software Installation

Contact

Chris Field

Session 1

• Sequence Data
  • Data formats
    • Raw
    • FASTQ
    • FASTA
    • GENBANK
    • GFF
  • Sequence Databases
  • Exercises
• Alignment
  • BLAST
  • BLAST on the command line
  • Exercises

Session 2

• Quality Control
  • FASTQ
  • Paired-End Sequencing
  • Read Quality Control
    • Raw data
    • Adapter removal
    • PhiX removal
    • Low quality base/read removal
  • Exercises
• Short read alignment
  • Exercises

Session 3

• Assembly
  • SPAdes
  • Assembly Assessment
  • Exercises
• Annotation
  • ORF Finding
  • Protein Identification
    • Sequence Similarity
    • HMMs
  • Motif Finding
  • RNA Finding
  • Other
  • Exercises