cd-hit-454 protocols

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 No

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Publication for cd-hit-454

cd-hit-454 IN pipelines

 (6)
2015
PMCID: 4536692
PMID: 26272581
DOI: 10.1128/genomeA.00926-15

[…] 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 (9, 10), and then processed with cd-hit-454 (11). the nonredundant protein sequence ncbi database (db:nr) was downloaded locally, and rapsearch2 (12) was used to perform the protein homology search of the trimmed clustered reads […]

2014
PMCID: 4410273
PMID: 25333462
DOI: 10.1038/ismej.2014.198

[…] have been deposited at the ncbi sequence read archive under accession srx278429–srx278432 and srx278437., all metagenomic sequence libraries were filtered to remove artifical duplicate reads using cd-hit-454 (niu et al., 2010). metatranscriptomic sequences were compared against silva to remove 16s rrna (pruesse et al., 2007). we also aligned reads against an in-house database of rrna sequences […]

2013
PMCID: 3667073
PMID: 23734264
DOI: 10.1371/journal.pone.0065902

[…] (more than 4% of n) and very short sequences (less than 100 bp) were trimmed by using the lucy [31] and seqclean (http://compbio.dfci.harvard.edu/tgi/). the duplicated reads were eliminated by using cd-hit-454 software [32]. the pre-processed sequences were then subject to assembling using the program newbler v2.5.3 (roche 454 life sciences, branford, ct) with default assembly parameters. […]

2011
PMCID: 3041743
PMID: 21266061
DOI: 10.1186/1471-2164-12-59

[…] total of 14,087,315 roche 454 reads of the al8/78 genomic library were processed. after the removal of chloroplast and mitochondrial reads, artificial replicates of reads were filtered out using the cd-hit-454 program [27] at 98% alignment identity and 90% sequence coverage. artificial replicates are intrinsic artifacts of 454-based pyrosequencing occurring in all currently available 454 […]

2011
PMCID: 3060086
PMID: 21437280
DOI: 10.1371/journal.pone.0017693

[…] suggesting these may have been derived from amplification of organelle 16s sequences. to refine classification of these sequences, quality screened 16s reads were clustered using cd-hit-454s. cd-hit 454 reduces duplicate and nearly identical sequences from 454 datasets to a single consensus sequence identical to the longest read within specified parameters of similarity. default […]

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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