sickle

Windowed adaptive trimming for FASTQ files using quality scores

brewmacoslinux

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Windowed adaptive trimming for FASTQ files using quality

sickle

Trim single-end FASTQ file with default quality threshold$ sickle se -f input.fastq -o trimmed.fastq

Trim paired-end FASTQ files keeping only proper pairs$ sickle pe -f read1.fastq -r read2.fastq -o trim1.fastq -p trim2.fastq -s singles.fastq

Trim with custom quality threshold and window size$ sickle se -f input.fastq -o trimmed.fastq -q 25 -w 10