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FR-HIT specifications


Unique identifier OMICS_01850
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Some reference sequences and queries.
Input format FASTA,FASTQ
Output data Some recruitment results.
Operating system Unix/Linux
Programming languages C++
License MIT License
Computer skills Advanced
Version 0.7.1
Stability Stable
Maintained Yes




No version available


  • person_outline Weizhong Li

Publication for FR-HIT

FR-HIT citations


Genomics and prevalence of bacterial and archaeal isolates from biogas producing microbiomes

Biotechnol Biofuels
PMCID: 5684752
PMID: 29158776
DOI: 10.1186/s13068-017-0947-1

[…] ome sequences available for these BGPs (metagenome Accession Nos. at the NCBI database: SRA357208-09, SRA357211, SRA357213-14, SRA357221-23) were mapped on the genome sequences of these isolates with FR-HIT (v0.7; []) to sensitively recruit also metagenomic reads with lower sequence identity (global alignment down to 75% nucleotide sequence identity; Additional file ).As a baseline to compare agai […]


Adaptability as the key to success for the ubiquitous marine nitrite oxidizer Nitrococcus

Sci Adv
PMCID: 5665590
PMID: 29109973
DOI: 10.1126/sciadv.1700807

[…] dance of N. mobilis or Nitrococcus-like phylotypes.Selected OSD metagenomes, Tara, and MG-RAST samples were mapped to the N. mobilis Nb-231 genome (accession no. gi|211606481|ref|NZ_CH672427.1) using FR-HIT version 0.7 with the following parameters: -e 0.001 -u 0 -p 8 -c 80 -m (dynamically set to 40% of average read length in a sample). Hits for nitrogen and sulfur cycling genes of interest were c […]


Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems

PMCID: 5385130
PMID: 28396823
DOI: 10.7717/peerj.3134

[…] non-overlapping 150 bp fragments to simulate the most common sequence read length in current metagenome projects, and mapped back to the intact “Ca. D. cowenii” and “Ca. D. audaxviator” genomes using FR-HIT with default parameters, restricting matches to the single top best hit. Percent similarities ranging from 70–100% were tested in one percent increments in order to quantify the frequency that […]


Delta proteobacterial SAR324 group in hydrothermal plumes on the South Mid Atlantic Ridge

Sci Rep
PMCID: 4782131
PMID: 26953077
DOI: 10.1038/srep22842

[…] ed genomes divided by the percentage of reads that recruited to the assembled metagenomes. All steps were carried out with default settings for bowtie2’s two stages (index building and alignment) and fr-hit. Fr-hit is able to successfully recruit more reads to the assembled contigs compared to bowtie2 and henceforth, we only refer to results obtained with fr-hit.For all the contigs assigned in thi […]


Metagenomic Surveys of Gut Microbiota

PMCID: 4563348
PMID: 26184859
DOI: 10.1016/j.gpb.2015.02.005

[…] data .CAMERA and WebMGA are also frequently used web servers for metagenomic data analysis. CAMERA offers a list of workflows, but many useful tools are missing, such as Filter-HUMAN, RDP-binning, FR-HIT-binning, and CD-HIT-OTU, which are otherwise available with WebMGA. Filter-HUMAN is a tool for filtering human sequences from human microbiome samples. RDP-binning uses the binning tool from Ri […]


Mining for viral fragments in methylation enriched sequencing data

Front Genet
PMCID: 4316777
PMID: 25699076
DOI: 10.3389/fgene.2015.00016

[…] o be detected. Moreover, it is capable of revealing epigenetic information about the clinical virus biology. Our method is generic and could be used in combination with other NGS techniques. However, FR-HIT does not account for splicing events which might restrict its applicability to RNA-seq data.The outlined approach was used on cervical samples of different origin, both histologically and study […]


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FR-HIT institution(s)
Center for Research in Biological Systems, University of California San Diego, La Jolla, CA, USA
FR-HIT funding source(s)
Supported by Awards (R01RR025030 and R01HG005978) from National Center for Research Resources and National Human Genome Research Institute.

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