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CD-HIT specifications

Information


Unique identifier OMICS_05157
Name CD-HIT
Alternative names CD-HIT-EST, cdhit-est
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained No

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Information


Unique identifier OMICS_05157
Name CD-HIT
Alternative names CD-HIT-EST, cdhit-est
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained No

Publications for CD-HIT

CD-HIT citations

 (1291)
library_books

Transcriptome and Co Expression Network Analyses Identify Key Genes Regulating Nitrogen Use Efficiency in Brassica juncea L.

2018
Sci Rep
PMCID: 5945678
PMID: 29748645
DOI: 10.1038/s41598-018-25826-6

[…] ing from 19–71 based on good quality read sequences and corresponding contigs/scaffolds were produced for each k-mer. Tool GapCloser was used to close the gaps emerged during the scaffolding process. CD-HIT-EST version 4.6, a clustering program was used to search similar sequences with minimum similarity cut-off of 90% (http://weizhongli-lab.org/cd-hit). Another clustering step was performed using […]

library_books

The aquatic animals’ transcriptome resource for comparative functional analysis

2018
BMC Genomics
PMCID: 5954267
PMID: 29764375
DOI: 10.1186/s12864-018-4463-x

[…] we optimized the de novo assembly pipeline of RNA-seq data [] by combining Oases, SOAPdenovo-Trans, and Trinity assemblers. To obtain complete transcriptomes from various assemblers [, ], we used the CD-HIT-EST cluster tool to merge Oases, SOAPdenovo-Trans, and Trinity assembling results. This combinational approach significantly reduce the transcript number and keeping a representative sequence f […]

library_books

Transcriptomic analysis of crustacean molting gland (Y organ) regulation via the mTOR signaling pathway

2018
Sci Rep
PMCID: 5943448
PMID: 29743490
DOI: 10.1038/s41598-018-25368-x

[…] ion 4.4, <3 CPM in replicate libraries). EdgeR filtering ensured that genes were retained when consistently expressed in all replicate libraries. EdgeR filtering retained 33.61% (69,002) of the total CD-HIT assembled transcriptome (Table ). This was designated as the reference transcriptome (YO/I/DRESA) (Fig.  and Table ). Statistics characterizing the reference transcriptome assembly process are […]

library_books

Salmonella enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping

2018
Front Microbiol
PMCID: 5945981
PMID: 29780368
DOI: 10.3389/fmicb.2018.00836

[…] itidis isolates we used 100% sequence identity and alignment coverage for comparing the prophage profiles of S. Enteritidis outbreak isolates. The representative sequence of each cluster generated by CD–HIT-EST was used to determine the prophage identity of that cluster by local alignment of the sequences against the PHASTER prophage virus database using BLASTX (Altschul et al., ). A prophage clus […]

library_books

Novel sequences, structural variations and gene presence variations of Asian cultivated rice

2018
Sci Data
PMCID: 5931083
PMID: 29718005
DOI: 10.1038/sdata.2018.79

[…] d contigs with length >500 bp from each rice accession were merged into a single sequence set. Next, CD-HIT v4.6.123 was used to remove redundant sequences at an identity cut-off of 90% with command “cd-hit-est -i input.fa -o output.fa -c 0.9 -T 16 -M 50000”. This process was carried out for 3 times to ensure redundancies were removed. Next, various contaminants including archaea, bacteria, virus, […]

library_books

MIKCC type MADS box genes in Rosa chinensis: the remarkable expansion of ABCDE model genes and their roles in floral organogenesis

2018
PMCID: 5928068
PMID: 29736250
DOI: 10.1038/s41438-018-0031-4

[…] luding SMART (http://smart.embl-heidelberg.de/) and Pfam to confirm the integrity of the MADS-box domains. Finally, the corresponding nucleotide sequences of all candidate genes were submitted to the CD-HIT Suite server, with 90% sequence identity cut-off (http://weizhong-lab.ucsd.edu/cdhit_suite/cgi-bin/index.cgi?cmd=Server%20home) to remove redundant sequences along with manual checking (Supplem […]

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CD-HIT institution(s)
Center for Research in Biological Systems, University of California San Diego, La Jolla, CA, USA

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