cd-hit-454 protocols

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cd-hit-454 specifications

Information


Unique identifier OMICS_01037
Name cd-hit-454
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Roche
Operating system Unix/Linux
Computer skills Advanced
Stability No
Maintained Yes

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Maintainer


  • person_outline Weizhong Li <>

Publication for cd-hit-454

cd-hit-454 in pipelines

 (13)
2018
PMCID: 5855864
PMID: 29495282
DOI: 10.3390/ijms19020642

[…] and 99% had a length of 40 ± 3 nt., the pre-processed sequence data set (ngs pool, 2597 sequences) was further analyzed by a two-step clustering and alignment method. clustering was done using the cd-hit-454 program []. the data set was first clustered at 100% identity (n = 10) to make a reduced non-redundant data set. duplicate sequences and orphans were identified and sorted with respect […]

2016
PMCID: 4712596
PMID: 26764021
DOI: 10.1186/s12864-016-2380-4

[…] using powersoil dna isolation kit (mobio laboratories). shotgun metagenome sequencing was performed using the gs flx+ system according to the supplier’s protocol. duplicated reads were removed by cd-hit-454 []., taxonomic assignment was performed using kraken [] against complete prokaryotic genomes from refseq []. cds prediction was performed using metaprodigal []. cdss less than 30 amino […]

2016
PMCID: 5108929
PMID: 27895627
DOI: 10.3389/fmicb.2016.01790

[…] collected from a hospital located in south zone were named sz and samples gathered from the hospital in north zone were named nz. raw reads were trimmed for 454 inherent artifacts removal using cd-hit-454 (version 4.5.4, default parameter, and 98% of identity option) () and filtered by quality (phred quality -q = or > 20) and length (>100 bp) using lucy program (version 1.2) (). […]

2015
PMCID: 4536692
PMID: 26272581
DOI: 10.1128/genomeA.00926-15

[…] of 40 to 1,074 bases (nt) (520 nt average)., raw sequence reads were trimmed using a custom application for removing nucleotides derived from the amplification primers (, ), and then processed with cd-hit-454 (). the nonredundant protein sequence ncbi database (db:nr) was downloaded locally, and rapsearch2 () was used to perform the protein homology search of the trimmed clustered reads […]

2013
PMCID: 3634838
PMID: 23637924
DOI: 10.1371/journal.pone.0061890

[…] reads (<200 bp or phred quality scores <20) were removed from the metagenomic library. identical reads that were generated as artifacts during pyrosequencing were also removed using the cd-hit-454 identifiers . remaining sequences were analyzed by blastn against the rdpii database to identify putative rrna gene sequences (cutoff value of e <10−5). the taxonomic affiliations […]


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cd-hit-454 in publications

 (41)
PMCID: 5855864
PMID: 29495282
DOI: 10.3390/ijms19020642

[…] and 99% had a length of 40 ± 3 nt., the pre-processed sequence data set (ngs pool, 2597 sequences) was further analyzed by a two-step clustering and alignment method. clustering was done using the cd-hit-454 program []. the data set was first clustered at 100% identity (n = 10) to make a reduced non-redundant data set. duplicate sequences and orphans were identified and sorted with respect […]

PMCID: 5775200
PMID: 29352122
DOI: 10.1038/s41598-017-18889-4

[…] at −80 °c., whole-genome sequencing of arthrobacter sp. cgmcc 3584 was performed using the roche 454 genome sequencer flx system (majorbio, shanghai, china). after the removal of duplications (by cd-hit-454), the clean data were assembled using gs assembler. the finished results were analyzed and annotated using glimmer, genemarker, gismo, epos-blastview, blast2go, trnascan-se, rnammer. […]

PMCID: 5704599
PMID: 29179741
DOI: 10.1186/s40168-017-0374-3

[…] for microbial metagenomes, trimmomatic [] (version 0.33) was used to trim remaining adaptor sequences and retain sequences with a minimum length of 85 bp. artificial duplicates were removed using cd-hit-454 []. due to biases associated with transposon tagementation, further quality control steps were used for viral metagenomes to ensure removal of excess sequence duplications, high coverage […]

PMCID: 5660117
PMID: 29079803
DOI: 10.1038/s41467-017-01265-1

[…] sequences. ambiguous reads and homopolymers consisting of five or more base pairs (bp) were removed using ambiguityfiltering.pl and homopolymertrimming.pl scripts of ngs qc toolkit, respectively. cd-hit-454 was used to remove possible artificial duplicates at a 99% threshold. at each step, short sequences (<200 bp) were removed. finally, 16s rrna sequences were predicted using sortmerna […]

PMCID: 5649160
PMID: 28731469
DOI: 10.1038/ismej.2017.102

[…] contigs ⩾600 bp were analyzed in this study., pyrosequencing reads from the norway and north sea viromes were first filtered to remove sequences with ⩾7% ambiguous bases and duplicate reads using cd-hit-454 at 99% identity (). residual adapter sequences were trimmed from the reads, and any reads showing homology to sequences in the univec database (e-value cutoff ⩽10−75) were removed. […]


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cd-hit-454 institution(s)
California Institute for Telecommunications and Information Technology, University of California, San Diego, CA, USA; Center for Research in Biological Systems, University of California San Diego, San Diego, CA, USA
cd-hit-454 funding source(s)
Supported by Award Number R01RR025030 from the National Center for Research Resources (NCRR).

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