Step 1.2: Quality trimming
Once the adapters have been trimmed, it is useful to inspect the quality of reads in bulk, and try to trim low quality nucleotides 1. Also, frequently the quality tends to drop off toward one end of the read. FASTQC 2 and PrinSeq 3 will show that very nicely . These read ends with low average quality can then be trimmed, if desired, using Trimmomatic 4, FASTX-Toolkit fastq_quality_filter, PrinSeq, or SolexaQA 5.
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