sickle ☆
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Description:
Windowed adaptive trimming for FASTQ files using quality
Type: Formula  |  Tracked Since: Dec 28, 2025
Links: Homepage  |  formulae.brew.sh
Category: Other
Tags: bioinformatics fastq trimming genomics sequencing
Install: brew install sickle
About:
Sickle is a bioinformatics tool designed for quality trimming and adapter trimming of sequencing reads in FASTQ files. It uses a sliding window approach to dynamically trim low-quality bases from the ends of reads, ensuring high-quality data for downstream analysis. This significantly improves the accuracy of genome assemblies and variant calling by removing unreliable sequence data.
Key Features:
  • Sliding window quality trimming
  • Adapter trimming support
  • Paired-end read handling
  • Multiple quality score formats (Sanger, Illumina)
Use Cases:
  • Preparing raw sequencing data for genome assembly
  • Trimming reads for accurate variant calling
  • Cleaning up low-quality regions in RNA-seq data
Alternatives:
  • Trimmomatic – More feature-rich with additional options like palindrome adapter trimming, but Sickle is simpler and faster for basic quality trimming.
  • Cutadapt – Primarily focused on adapter removal but also does quality trimming; Sickle is often preferred for its sliding window approach to quality.
Version History
Detected Version Rev Change Commit
Sep 15, 2025 9:23am 0 VERSION_BUMP bd5edaa3
Sep 14, 2024 5:07am 0 VERSION_BUMP 058b40c9
Nov 26, 2022 1:57am 0 VERSION_BUMP 21a67fb2
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