FastUniq protocols

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FastUniq specifications


Unique identifier OMICS_01044
Name FastUniq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Sequence files.
Input format FASTQ
Output data Unique read pairs into two sequence files with reads in the same order belonging to a pair.
Output format FASTQ or FASTA
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Jinhui Chen <>
  • person_outline Shilin Chen <>

Publication for FastUniq

FastUniq in pipelines

PMCID: 5805368
PMID: 29377900
DOI: 10.1371/journal.pgen.1007183

[…] were preprocessed in three steps before using them for extending pacbio contigs: a) using trimmomatic [], from both ends of reads, nucleotides with base quality lower than 15 were removed. b) using fastuniq [], duplicate pairs were removed from the pe library, and c) soapec [] was used to correct read error [, ]. any initial genome sequence has bacterial contamination due, at least, […]

PMCID: 5924919
PMID: 29643074
DOI: 10.1073/pnas.1721381115

[…] in dataset i, including the first sample, which is technically a vegetative mycelium sample. the compost dataset exhibited high amounts of pcr duplicates (si appendix n), which we removed using fastuniq ()., the p1 and p2 genomes () were annotated with braker1 () and augustus 3.0.2 () using the pooled rna-seq data from the mushroom tissue dataset (si appendix o). named genes are provided […]

PMCID: 5278356
PMID: 28134354
DOI: 10.1038/srep41659

[…] diego, ca, usa) following the 100 bp paired-end genomic dna sequencing protocol., the sequence reads from chip and input dnas (chip-seq and input-seq reads, respectively) were first treated using fastuniq and trimmomatic to remove pcr duplication and low quality reads. a two-step procedure was adopted with some modifications to determine the centromeric repetitive sequences. first, the input […]

PMCID: 5322946
PMID: 28231340
DOI: 10.1371/journal.pone.0171311

[…] housed at the queensland university of technology, central analytical research facility (qut carf). raw reads were filtered prior to alignment; trimmomatic [] was used to only keep reads of 150 nt, fastuniq was used to remove pcr duplicates and bbsplit from the bbmap package ( was used to remove reads aligning to mitochondria and chloroplast genomes […]

PMCID: 5332604
PMID: 28261669
DOI: 10.1128/mSphere.00359-16

[…] used raw reads for the above assemblies, but the reads underwent a quality-control screening before being back-mapped to contigs with the following procedure: (i) duplicated reads were removed using fastuniq (); (ii) paired-end reads were merged with flash, and the merged and unmerged reads were kept; (iii) reads were removed if the percentage of high-quality nucleotide positions (i.e., quality […]

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FastUniq in publications

PMCID: 5874918
PMID: 29588409
DOI: 10.1128/mBio.02430-17

[…] using the illumina technology, obtaining paired-end 150-bp sequences for the 300-bp inserts by genewiz (usa). raw data were trimmed with trimmomatic (v2.4.0), and the pcr duplicates were removed by fastuniq (v1.1). high-quality data were mapped to the reference genome using bowtie2 (v2.3.0). the mapped data were called by gatk (v3.7) and samtools (v1.4) for variant analysis, including single […]

PMCID: 5916287
PMID: 29721275
DOI: 10.1002/ece3.3918

[…] et al. () with some modifications. specifically, adapter trimming for mate‐pair sequences was performed using nxtrim v0.3.0‐alpha (o'connell et al., ), and all filtered reads were analyzed with fastuniq v1.1 (xu et al., ) to remove putative pcr duplications. the overall quality of all sequence reads was evaluated before and after postsequencing quality control using fastqc (andrews, )., […]

PMCID: 5845502
PMID: 29682127
DOI: 10.1155/2018/1857170

[…] for cdna library construction and sequencing. raw data were processed by filtering low-quality reads by solexaqa v2.0 (defaults to p=0.05, or equivalently q = 13) and removing the pcr duplicates by fastuniq v1.1 with default settings. high-quality clean reads were then assembled by allpaths-lg v41245 [] with default settings. gapcloser v1.12 from soapdenovo2 package [] was used to close gaps […]

PMCID: 5833558
PMID: 29374141
DOI: 10.1038/s41419-017-0141-1

[…] reads was firstly checked with fastqc (version 0.11.2) low quality bases (q < 20) on 3′ ends of reads were trimmed off using seqtk (version 1.0). duplicated reads were then removed with fastuniq (version 1.1) before mapping to the human reference genome grch37 with bwa (version 0.7.6.a). the alignments were refined with tools of the gatk suite (version 3.2). variants were called […]

PMCID: 5773036
PMID: 29343235
DOI: 10.1186/s12864-018-4434-2

[…] grape (bioproject accession #275778) [] were downloaded and used for gene prediction in ap, plat_d, merge, and plat*_gc assemblies., before genome assembly, duplicate illumina reads were removed by fastuniq []. reads were corrected using quake [] with the following parameters: minimum length of reads ≥ 70 bp and minimum quality ≥ 20. the filtered reads were used to identify heterozygosity using […]

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FastUniq institution(s)
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
FastUniq 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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