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  • Quality Trimming read loss - Trimmomatic

    Hello community,

    I plan to do a reference assisted genome assembly for a yeast genome.
    I have some questions regarding the trimming prior the assembly:

    # Setup:
    Illumnia MiSeq / Paired end sequencing / coverage around 80x

    # Case:
    Intended pipeline:
    raw reads --> trimming --> Spades or Velvet --> Contiguator

    I ran FastQC on the raw reads (see attached files, forward reads shown):
    FastQC does not detect adapters.
    Since the quality drops in the end of the reads, so I decided to use trimmomatic for quality trimming.

    I needed to apply a strict quality cutoff in order to obtain better FastQC results (see attachements). I used following parameters in trimmomatic:
    Code:
    SLIDINGWINDOW:4:30 HEADCROP:11 MINLEN:40
    However, I recognized a huge loss of reads after the trimming :

    Raw reads: 9322401
    trimmed reads: 7320129
    -> loss of 21 %

    # Questions:
    1. Since FastQC did not detect illumina adapters in the raw reads, would you still run a adapter removing step (eg AdapterRemoval or trimmomatic [ILLUMINACLIP])?

    2. What would you suggest regarding the quality trimming? Some people suggest not to run any trimming at all. Should I go down with the cutoff values in order to keep more reads?

    Best regards
    Attached Files

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