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FastUniq | A de novo duplicates removal tool for paired short reads

Removes duplicates in paired short reads. FastUniq compares sequences between read pairs to identify duplicates. The software can be used with flexibility in almost all next-generation sequencing (NGS)-based studies, and is capable of simultaneously handling reads with different lengths. It thus provides an opportunity to remove duplicates in multiple sequencing results from one library and to be integrated into the mainstream NGS processing pipelines.

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FastUniq classification

FastUniq specifications

Unique identifier:
Command line interface
Input data:
Sequence files.
Output data:
Unique read pairs into two sequence files with reads in the same order belonging to a pair.
Operating system:
Computer skills:
Software type:
Restrictions to use:
Input format:
Output format:
Programming languages:

FastUniq distribution


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FastUniq support


  • Jinhui Chen <>
  • Shilin Chen <>


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The National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Nanjing Forestry University, Nanjing, China; Department of Geosciences, Stony Brook University, Stony Brook, NY, USA

Funding source(s)

Supported by the Key National Natural Science Foundation of China [Grant number 81130069], the Program for Changjiang Scholars and Innovative Research Team in University of Ministry of Education of China [Grant number IRT1150] and the National Science Foundation of China [Grant numbers
30901156, 31170619].

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