CLC Assembly Cell pipeline

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


  • Animals
    • Caenorhabditis elegans
    • Danio rerio
    • Homo sapiens
  • Eubacteria
    • Escherichia coli


  • CLCbio


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Additional information

CLC Assembly Cell citations

PMCID: 5946037

[…] software, on the set of 287 million sequence reads (2). 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 (3, 4)., a 14,420-nucleotide (nt) […]

PMCID: 5913325

[…] 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: 5855747

[…] 50; trailing: 3; leading: 3; and sliding window: 4:15. de novo assembly from c. edulis employed the default parameters (available online: in the clc genomic workbench v7 (clcbio, hilden, germany). then, three independent de novo assemblies, which included single-end forward reads, single end reverse reads, and pe reads, were performed [18]. after that, a single […]

PMCID: 5751910

[…] positions in the f2 map. in addition, all snp marker sequences from the consensus map were aligned to the nbi g hirsutum l. acc. tm-1 genome reference using clc genomics workbench 8.5.1 ( basic local alignment search tool (blast) with 50-word size, at least 95% dna sequence similarity and e < 1.0 × e−5., the illumina infinium genotyping cottonsnp63k array and cluster […]

PMCID: 5732179

[…] (andrews, 2010). high-throughput sequence raw data were imported into clc genomics workbench version 9.0.1 with plugins clc microbial genomics module version 1.3.1 (qiagen, aarhus a/s, according to quality scores from illumina pipeline 1.8, in order to achieve the highest quality sequences for clustering. sequence data were trimmed using 0.05 as a limit for quality […]

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