FR-HIT protocols

View FR-HIT computational protocol

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FR-HIT specifications

Information


Unique identifier OMICS_01850
Name FR-HIT
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

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Maintainer


  • person_outline Weizhong Li <>

Publication for FR-HIT

FR-HIT in pipeline

2011
PMCID: 3170331
PMID: 21931709
DOI: 10.1371/journal.pone.0024417

[…] for principal coordinates analysis (pcoa)., several quality control filters were applied to wgs raw reads before analysis. first, host contaminants (sequences of bovine origin) were removed using fr-hit against the bovine genome btau 4.0 (cutoff: 95% identity over 95% of the entire sequence length). the possible artifacts (redundant reads) were then identified and excluded using cd-hit . […]


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FR-HIT in publications

 (11)
PMCID: 5684752
PMID: 29158776
DOI: 10.1186/s13068-017-0947-1

[…] 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 […]

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

[…] 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 […]

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

[…] raw reads from the u1362a metagenome were mapped to the six scaffolds that make up the “ca. d. cowenii” genome bin and the “ca. d. audaxviator” genome. recruitment was performed using fr-hit v0.7.1 () with default parameters (minimum sequence similarity 75%) and reporting a single best top hit for each read (-r 1)., full length ssu rrna genes from the raw quality-filtered u1362a […]

PMCID: 4982221
PMID: 27525040
DOI: 10.1186/s13068-016-0581-3

[…] genomes as described recently []. therefore, the combined metagenome sequencing dataset (see above) was used, representing the thermophilic biogas-producing microbial community. afterwards, the fr-hit software tool [] was used to perform a global alignment against the completely sequenced genomes of the strains described above. an identity cutoff of 75 % was used to align the sequencing […]

PMCID: 4782131
PMID: 26953077
DOI: 10.1038/srep22842

[…] proteins assigned to sar324 cluster bacteria were subjected to the following annotation analyses. relative abundance of the binned sar324 was estimated by read recruitment using bowtie2 and fr-hit. the reads were recruited to the three assembled metagomes as well as to the four binned sar324 genomes. the abundance was derived from the percentage of successfully recruited reads […]


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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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