CLC bio pipeline

CLC bio specifications

Information


Unique identifier OMICS_01124
Name CLC bio
Alternative name CLC Genomics Workbench
Software type Pipeline/Workflow
Interface Command line interface, Graphical user interface
Restrictions to use License purchase required
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 10
Stability Stable
Free trial Yes
Maintained Yes

Versioning


Add your version

Documentation


Maintainer


  • person_outline CLC Genomics Workbench Team <>

CLC bio IN pipelines

 (412)
2018
PMCID: 5722268
PMID: 29236931
DOI: 10.1590/0074-02760170119

[…] spin kit (ge healthcare do brasil ltda, são paulo, brazil). whole-genome sequencing was performed through illumina™ miseq platform with 300 bp paired-end library. de novo assembly was performed with clc genomics workbench 7.5.1 (clc bio, denmark) and geneious 10.0.3 (biomatters ltd, auckland, new zealand)., the obtained contigs were ordered according to l. interrogans serovar copenhageni strain […]

2018
PMCID: 5722268
PMID: 29236931
DOI: 10.1590/0074-02760170119

[…] ltda, são paulo, brazil). whole-genome sequencing was performed through illumina™ miseq platform with 300 bp paired-end library. de novo assembly was performed with clc genomics workbench 7.5.1 (clc bio, denmark) and geneious 10.0.3 (biomatters ltd, auckland, new zealand)., the obtained contigs were ordered according to l. interrogans serovar copenhageni strain fiocruz l1-130 reference […]

2018
PMCID: 5756330
PMID: 29304737
DOI: 10.1186/s12864-017-4415-x

[…] length of 2 × 75 bases were generated. primary transcriptome libraries were sequenced in single read mode with a read length of 35 or 75 bases., read processing and mapping was carried out with the clc genomics workbench (qiagen aarhus a/s). reads were trimmed by removing adapter sequences using the trim sequences tool and filtered for phred quality scores <30 [40]. reads from primary […]

2018
PMCID: 5758643
PMID: 29311719
DOI: 10.1038/s41598-017-18445-0

[…] and overall quality was improved by trimming the reads using trimmomatic121, with following parameters: crop = 95, headcrop = 10, minlen = 85., high quality rna-seq reads were mapped using the clc genomics workbench (v. 9.5.3)., traces of ribosomal rna contamination were removed from all libraries by mapping against sunflower ribosomal sequences downloaded from the ncbi database […]

2018
PMCID: 5766512
PMID: 29330490
DOI: 10.1038/s41598-017-18607-0

[…] pirna (http://www.ncbi.nlm.nih.gov/and http://pirnabank.ibab.ac.in/) and rfam database (http://rfam.sanger.ac.uk/) with a tolerance of two mismatches using the software of clc genomics_workbench 5.5. sequences that did not overlap with any annotated sequence were classified as unannotated reads. next, the annotated small rnas varying between 18 to 35 nt were classified […]

CLC bio reviews

 (2)
star_border star_border star_border star_border star_border
star star star star star

Arup Ghosh

star_border star_border star_border star_border star_border
star star star star star
Desktop
For wet lab biologists, CLC workbench is a great tool for analyzing next-generation sequencing datasets. Most of the analysis pipelines are predefined, so very less time wasted on setup process. Also one can easily manipulate existing pipelines according to their convenience.

salvador_angel

star_border star_border star_border star_border star_border
star star star star star
Desktop
I've bee using this software for years and I have found its solution as one of the best in the class of bioinformatics workbenches although I have found that its usage is very limited many cases due to the cost of the software that it's licensing represent for many labs. Nonetheless this workbench allows to get a free-limited versio that is still very usefull for doing general sequence visualization and organization tasks. It provides both a Server and a Client implementation so is very scalable and compatible with all main OS.