NGSUtils

NGSUtils is a set of software tools that can manipulate data types used in next-generation sequencing, such as FASTQ, BED, and BAM. The software is modular, stable and provides a platform for data management and analysis. NGSUtils is available under a BSD license and works on Mac OS X and Linux systems. It requires Python 2.6+ and virtualenv.

Topic

Genomics;Transcriptomics

Detail

  • Operation: Read pre-processing;Sequencing quality control;Variant calling;Formatting;Sequence contamination filtering

  • Software interface: Suite

  • Language: Python

  • License: BSD 3-Clause "New" or "Revised" License

  • Cost: Free

  • Version name: FASTA/FASTQ

  • Credit: National Institutes of Health, Indiana Biobank, the Indiana Clinical and Translational Sciences Institute, NCRR Clinical and Translational Sciences Award.

  • Input: GFF, GTF, FASTA/FASTQ

  • Output: -

  • Contact: mbreese@stanford.edu;yunliu@iu.edu

  • Collection: -

  • Maturity: Stable

Publications

  • NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets.
  • Breese MR and Liu Y. NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets. NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets. 2013; 29:494-6. doi: 10.1093/bioinformatics/bts731
  • https://doi.org/10.1093/bioinformatics/bts731
  • PMID: 23314324
  • PMC: PMC3570212

Download and documentation

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