Atropos

Atropos is a high-performance software tool for trimming adapter sequences and low-quality bases from raw sequencing reads. It aims to improve the quality and reliability of downstream analyses while reducing computational requirements. Compared to other state-of-the-art read trimming tools, Atropos offers superior trimming accuracy without compromising execution speed, even when dealing with data containing high rates of sequencing errors. Its broad feature set and high performance make it suitable for pre-processing various short-read sequencing datasets, including those generated by Illumina and ABI SOLiD platforms.

Topic

Sequencing;Bioinformatics;Sequence assembly

Detail

  • Operation: Read pre-processing;Sequence trimming;k-mer counting;Read mapping

  • Software interface: Command-line user interface

  • Language: Python

  • License: Other

  • Cost: Free of charge with restrictions

  • Version name: 1.1.32

  • Credit: NIH intramural program, American Diabetes Association, Knut and Alice Wallenberg Foundation.

  • Input: -

  • Output: -

  • Contact: John P. Didion john.didion@nih.gov

  • Collection: -

  • Maturity: Stable

Publications

  • Atropos: specific, sensitive, and speedy trimming of sequencing reads.
  • Didion JP, et al. Atropos: specific, sensitive, and speedy trimming of sequencing reads. Atropos: specific, sensitive, and speedy trimming of sequencing reads. 2017; 5:e3720. doi: 10.7717/peerj.3720
  • https://doi.org/10.7287/PEERJ.PREPRINTS.2452V2
  • PMID: 28875074
  • PMC: PMC5581536

Download and documentation

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