CLC Assembly Cell 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


Add your version

Additional information


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

CLC Assembly Cell IN pipelines

 (72)
2018
PMCID: 5855747
PMID: 29425128
DOI: 10.3390/ijms19020525

[…] the parameters used were as follows: minlen: 50; trailing: 3; leading: 3; and sliding window: 4:15. de novo assembly from c. edulis employed the default parameters (available online: http://www.clcbio.com) 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, […]

2018
PMCID: 5855747
PMID: 29425128
DOI: 10.3390/ijms19020525

[…] 50; trailing: 3; leading: 3; and sliding window: 4:15. de novo assembly from c. edulis employed the default parameters (available online: http://www.clcbio.com) 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 […]

2018
PMCID: 5946037
PMID: 29748415
DOI: 10.1128/genomeA.01438-17

[…] 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) […]

2017
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, […]

2017
PMCID: 5291366
PMID: 28158238
DOI: 10.1371/journal.pone.0171187

[…] performed using fastqc. before using the rna-seq reads for de novo assembly, a create sequencing qc report was run using clc genomics workbench v7.5.1 (following called clc; qiagen aarhus a/s; www.clcbio.com) to produce the quality reports. low-quality sequences and the adaptors were trimmed using trim sequences tools in clc, and then the trimmed sequences were checked by running the create […]

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