CAP3 statistics

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Citations per year

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Popular tool citations

chevron_left Genome assembly Read alignment De novo transcriptome assembly chevron_right
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CAP3 specifications

Information


Unique identifier OMICS_12802
Name CAP3
Interface Web user interface
Restrictions to use None
Input format FASTA
Computer skills Basic
Version 3.0
Maintained No

Maintainer


This tool is not maintained anymore.

Publication for CAP3

CAP3 in pipelines

 (204)
2018
PMCID: 5821328
PMID: 29466388
DOI: 10.1371/journal.pone.0192377

[…] control for illumina processing [] were removed and not considered in subsequent analyses., non-phage virus sequences from each library identified from the blastx analysis were assembled using the cap3 algorithm [] in the vector nti contigexpress program (invitrogen, carlsbad, ca). sequences from phage were not assembled because they infect bacteria and would not be expected to infect fire ant […]

2018
PMCID: 5828125
PMID: 29732244
DOI: 10.1002/aps3.1013

[…] information has been deposited in the national center for biotechnology information (ncbi) sequence read archive (accession no. srr6067069). the transcripts, with further processing and filtering by cap3 (minimum identity = 99%), yielded a set of 80,181 nonredundant sequences with an average length of 600.48 bp and an n50 length of 860 bp (huang and madan, ). simple sequence repeats (ssrs) […]

2017
PMCID: 5351058
PMID: 28292322
DOI: 10.1186/s40168-017-0251-0

[…] were de novo assembled using idba-ud (v1.1.2) [] with kmers ranging from 20 to 100 and an increment of 20 at each iterative process. contigs were then subjected to a second round of assembly using cap3 [] with default parameters to obtain longer contigs. the longest (≥1,000 bp) and most covered (≥5000 reads) contigs enriched through hybridization capture were aligned with blastn […]

2017
PMCID: 5397604
PMID: 28431015
DOI: 10.1093/dnares/dsw056

[…] we applied 19,532 5′ ests and 4,915 3′ ests to seqclean (http://sourceforge.net/projects/seqclean/), which validates and trims dna sequences. then, 19,487 5′ ests and 4,480 3′ ests were assembled by cap3 with the following parameters (mindistance = 100 bp and maxdistance = 15000 bp)., total dna from two fl-cdna libraries was prepared using the illumina truseq dna lt sample prep kit (illumina, […]

2017
PMCID: 5407641
PMID: 28448540
DOI: 10.1371/journal.pone.0176337

[…] sequences from ests using vecscreen and estclean tool of ncbi. a summary of unigene statistics has been illustrated in . trimming resulted in 244 good quality sequences which were assembled using cap3 [] program into 134 non-redundant unigene sequences. of these, 106 were singletons whereas the remaining was assembled into 28 contigs. the unigene length ranged from 102–1156 base pair (bp) […]


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CAP3 in publications

 (608)
PMCID: 5954267
PMID: 29764375
DOI: 10.1186/s12864-018-4463-x

[…] organisms without draft genome., to improve the assembly quality, three computational tools (trinity, oases and soapdenovo-trans) were employed to enhance individual transcriptome assembly, and cap3 and cd-hit-est software were then used to merge these three assembled transcriptomes. in addition, functional annotation analysis provides valuable clues to gene characteristics, including […]

PMCID: 5943621
PMID: 29774017
DOI: 10.3389/fmicb.2018.00872

[…] remaining features were ranked according to the variable importance measures of breiman’s random forests method (), and the top features were adopted to design a random forests classifier., using cap3 (), the identified group-specific k-mers based on logical and numerical features were, respectively, assembled to longer sequences. for quality control, the assembled sequences longer […]

PMCID: 5908936
PMID: 29674552
DOI: 10.1128/genomeA.00301-18

[…] reads of 250 nucleotides (nt)., the reads were evaluated for quality and had their sequencing adapters removed using trimmomatic v0.32 (). the de novo assembly was made with mira v4.0-1 () and cap3 (), which generated 23 contigs and a draft genome of 8.4 mb. the n50 value obtained was 574,923 bp, the genome was 95.06% of the b. gladioli atcc 10248 reference genome size (), and the g+c […]

PMCID: 5919021
PMID: 29652888
DOI: 10.1371/journal.pntd.0006410

[…] previously using the assemblers abyss and soapdenovo-trans with every kmer ending in 1 and 5 (-k program switch) from 21 to 95 [–]. resulting contigs were re-assembled by a pipeline of blastn and cap3 assembler [] as described earlier []. coding sequences were extracted based on blastx [] results deriving from several database matches, including a subset of the non-redundant protein database […]

PMCID: 5861484
PMID: 29560829
DOI: 10.1186/s12918-018-0548-z

[…] sets, we used the trinity in silico normalization. all parameters were set as default. as a result 62.9 million base pairs and 744,507 contigs were assembled. we further performed scaffolding using cap3 [] to acquire a total of 613,448 scaffolded contigs. to compensate for sequence variations caused by sub-species difference, our transcriptome rna-seq reads were used to build sample specific […]


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CAP3 institution(s)
Department of Computer Science, Michigan Technological University, Houghton, MI, USA; Department of Molecular Biotechnology, University of Washington, School of Medicine, Seattle, WA, USA
CAP3 funding source(s)
National Institutes of Health grant R01 HG01502-03

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