FastUniq protocols

FastUniq specifications

Information


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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Maintainers


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

Publication for FastUniq

FastUniq IN pipelines

 (7)
2018
PMCID: 5805368
PMID: 29377900
DOI: 10.1371/journal.pgen.1007183

[…] preprocessed in three steps before using them for extending pacbio contigs: a) using trimmomatic [63], from both ends of reads, nucleotides with base quality lower than 15 were removed. b) using fastuniq [64], duplicate pairs were removed from the pe library, and c) soapec [65] was used to correct read error [64, 65]. any initial genome sequence has bacterial contamination due, at least, […]

2018
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 (32)., the p1 and p2 genomes (13) were annotated with braker1 (33) and augustus 3.0.2 (34) using the pooled rna-seq data from the mushroom tissue dataset (si appendix o). named genes […]

2017
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 fastuniq56 and trimmomatic57 to remove pcr duplication and low quality reads. a two-step procedure7 was adopted with some modifications to determine the centromeric repetitive sequences. first, […]

2017
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 (99); (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., […]

2017
PMCID: 5373778
PMID: 28251916
DOI: 10.1212/WNL.0000000000003772

[…] was fragmented, exome-enriched, and sequenced (illumina [san diego, ca] truseq 62 mb and hiseq 2000, 100 bp paired-end reads). bioinformatic analysis included duplicate sequence read removal with fastuniq,7 alignment to ucsc hg19 with bwa8 variant detection with freebayes, and variant annotation with annovar. variants were annotated as exonic/splicing, excluding synonymous variants, […]

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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