CLC Assembly Cell protocols

View CLC Assembly Cell computational protocol

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CLC Assembly Cell specifications


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


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


  • CLCbio


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Additional information

CLC Assembly Cell in pipelines

PMCID: 5806058
PMID: 29435426
DOI: 10.4102/ajlm.v7i1.658

[…] 45 seconds. sanger sequencing was performed by inqaba biotechnical industries (pretoria, south africa) in both directions on all 60 amplified products. the clc main workbench software program v6.0 (clcbio, waltham, massachusetts, united states) was used to analyse the sequences against the ncbi reference sequence ng_009904., lna, locked nucleic acid., indicates lna bases, wild-type and mutant […]

PMCID: 5867861
PMID: 29498712
DOI: 10.3390/genes9030140

[…] polymorphisms were detected through manual examination of sequence traces using bioedit version [] and sequence differences in multiple alignments using clc sequence viewer 6.9 ( different haplotypes were compared by constructing a phylogenetic maximum likelihood tree using mega 6.06 []. genetic parameters of polymorphism including number of haplotypes (h) […]

PMCID: 5946037
PMID: 29748415
DOI: 10.1128/genomeA.01438-17

[…] 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) […]

PMCID: 5289670
PMID: 28153884
DOI: 10.1128/genomeA.01446-16

[…] amplified using the ion chef system and then used for sequencing on an ion s5 xl instrument using a 540 chip and ion 540 kit-chef (thermo fisher scientific)., the sequence data was assembled using clc assembly cell (version 4.4.2). for sample s3, three contigs originating from sav were detected through a blast search to a reference genome (genbank accession no. dq366344). the three contigs, […]

PMCID: 5336659
PMID: 28259138
DOI: 10.1186/s12862-017-0904-4

[…] ta was analyzed through blast-searches (blastp) v.2.6.0+ in ncbi genbank. molecular weight was calculated based on the full-length transcripts (without signal peptide) using clc main workbench v.7.7 (clcbio, qiagen, aarhus, denmark;, to screen for putative gltx paralogs, a maximum likelihood analyses v.8.2.8 [] of different clones was performed (raxmlhpc-pthreads-avx, gtr + gamma  […]

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CLC Assembly Cell in publications

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

[…] 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 the functional domain region observed in each wrkys were scanned and explored using expasy-prosite ( []. the sequences were analyzed […]

PMCID: 5920170
PMID: 29700157
DOI: 10.1128/genomeA.00336-18

[…] 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, […]

PMCID: 5933799
PMID: 29684026
DOI: 10.1371/journal.pntd.0006433

[…] 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 […]

PMCID: 5913325
PMID: 29719531
DOI: 10.3389/fimmu.2018.00605

[…] 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 ( 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 […]

PMCID: 5911478
PMID: 29713312
DOI: 10.3389/fendo.2018.00158

[…] 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 […]

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