CLC Assembly Cell statistics

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Citations per year

Number of citations per year for the bioinformatics software tool CLC Assembly Cell
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Tool usage distribution map

This map represents all the scientific publications referring to CLC Assembly Cell per scientific context
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Protocols

CLC Assembly Cell specifications

Information


Unique identifier OMICS_19504
Name CLC Assembly Cell
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use License purchase required
Output data A set of contig sequences or a file in a special format called cas.
Output format FASTA
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 5.0.4
Stability Stable
Maintained Yes

Taxon


  • Bacteria
    • Escherichia coli
  • Invertebrates
    • Caenorhabditis elegans
  • Primates
    • Homo sapiens
  • Vertebrates
    • Danio rerio

Subtool


  • CLCbio

Versioning


No version available

Additional information


http://resources.qiagenbioinformatics.com/manuals/clcassemblycell/current/index.php

CLC Assembly Cell citations

 (560)
call_split

Draft Genome Sequence of a Novel Rhabdovirus Isolated from Deinocerites Mosquitoes

2018
Genome Announc
PMCID: 5946037
PMID: 29748415
DOI: 10.1128/genomeA.01438-17
call_split See protocol

[…] discovery software, on the set of 287 million sequence reads (). After subtraction of sequences with an alignment to Culicidae and human sequences in GenBank, 90 million nonhost reads remained. Using CLC Assembly Cell (Qiagen), Pickaxe assembled the 78 million nonhost reads into 34,956 contigs that were subsequently annotated using a BLAST+/RAPSearch pipeline (, ).A 14,420-nucleotide (nt) contig w […]

library_books

Structural and functional dissection of differentially expressed tomato WRKY transcripts in host defense response against the vascular wilt pathogen (Fusarium oxysporum f. sp. lycopersici)

2018
PLoS One
PMCID: 5927432
PMID: 29709017
DOI: 10.1371/journal.pone.0193922

[…] ologs of the SolyWRKY33 and SolyWRKY37 was done to find out the percent consensus and conserved residues along the length of the entire protein in different members using CLC bio workbench http://www.clcbio.com. The functional domain region observed in each WRKYs were scanned and explored using ExPASy-Prosite (http://prosite.expasy.org/scanprosite/) []. The sequences were analyzed against the Inte […]

call_split

Draft Genome Sequence of the First South South Korean Clinical Isolate of Burkholderia pseudomallei, H0901

2018
Genome Announc
PMCID: 5920170
PMID: 29700157
DOI: 10.1128/genomeA.00336-18
call_split See protocol

[…] s the sequencing platform. A total of 7,956,141 reads were obtained by whole-genome sequencing, and fold coverage was 235. Finally, 142 contigs were assembled from all reads in CLC Genomic Workbench (CLCbio, version 10.0) using thresholds with a minimum of 500 bp (). The number of N50 contigs was 88,367. The draft genome of the H0901 strain consisted of 7,001,996 bp of nucleotides (G+C content, 68 […]

call_split

Entomopathogenic fungal infection leads to temporospatial modulation of the mosquito immune system

2018
PLoS Negl Trop Dis
PMCID: 5933799
PMID: 29684026
DOI: 10.1371/journal.pntd.0006433
call_split See protocol

[…] ng the aforementioned oligonucleotide primers. Resulting DNA sequences were visually edited and assembled using Sequencer 5.4 software (Gene Codes Corporation). Consensus sequences were aligned using CLCBio genomics workbench 9.0 software (Qiagen Inc.). Phylogenetic analysis was performed in MEGA 7 [] using the Maximum Likelihood method with a General Time Reversible model. The complete deletion o […]

call_split

Characterization of Chicken Tumor Necrosis Factor α, a Long Missed Cytokine in Birds

2018
Front Immunol
PMCID: 5913325
PMID: 29719531
DOI: 10.3389/fimmu.2018.00605
call_split See protocol

[…] non-avian vertebrate TNF-α genes were used as probes in BLAST searches of the SRA datasets. The sequences obtained were downloaded and assembled manually either with CLC genomics workbench 8.0.1 (www.clcbio.com) or with Lasergene 10.0.0 (DNASTAR, Madison, WI, USA). The resulting short contigs were used as probes in subsequent rounds of BLAST searches against SRA datasets, until the full open readi […]

call_split

Integrated Characterization of MicroRNA and mRNA Transcriptome in Papillary Thyroid Carcinoma

2018
PMCID: 5911478
PMID: 29713312
DOI: 10.3389/fendo.2018.00158
call_split See protocol

[…] equencing, preprocessing of data were conducted on Torrent Server using Torrent Suite v4.4.2 software (Life Technologies, USA) and FASTQ files were generated and then exported for data analysis using CLCBio Genomics Workbench v8.3 (CLC Bio, Denmark). The manufacturer’s analysis pipeline for transcriptome sequencing was used for differential expression of mRNA. Briefly, the pipeline includes remova […]


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CLC Assembly Cell institution(s)
QIAGEN Aarhus, Aarhus C, Denmark

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