CG-Pipeline protocols

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CG-Pipeline specifications

Information


Unique identifier OMICS_04062
Name CG-Pipeline
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline I. King Jordan <>

Publication for CG-Pipeline

CG-Pipeline in pipeline

2014
PMCID: 4110763
PMID: 25013135
DOI: 10.1128/genomeA.00617-14

[…] scaffolded using sopra version 1.4.6 to give an assembly size of 3.98 mb, with an n50 of 363 kb (, ). the gene predictions and annotations were performed using the computational genomics pipeline (cg-pipeline) version 0.4 and rast (, ), which predicted and annotated 3,533 coding genes. the g+c content is 47.5%., a phylogeny was constructed based on core genes, and 2012el-1759 was found […]


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CG-Pipeline in publications

 (6)
PMCID: 4876609
PMID: 27242777
DOI: 10.3389/fmicb.2016.00766

[…] virulence gene finder, and the remaining set of 19 were used to validate the stx subtyper. the genomes were downsampled to 40x, 30x, 20x, and 10x coverage using the computational genomics pipeline (cg-pipeline; https://github.com/lskatz/cg-pipeline; katz et al., ). downsampled genomes were assembled and analyzed using the genotyping plug-in bionumerics v.7.5 with the settings outlined […]

PMCID: 4408324
PMID: 25908123
DOI: 10.1128/genomeA.00229-15

[…] 2.7; 454 life sciences, branford, ct). all gaps between the contigs were filled by pcr and sanger sequencing, and the complete genome sequences were assembled and analyzed using omiga 2.0 and the cg-pipeline software (). the final draft genomes consisted of circular chromosomes of 1,629,815 bp, 1,562,125 bp, and 1,629,114 bp in length for hpml01, hpml02, and hpml03, respectively, as well […]

PMCID: 4395055
PMID: 25792058
DOI: 10.1128/genomeA.00139-15

[…] generating 2 × 100 paired-end sequencing libraries with an average insert size of 945 bp., all sequence reads were filtered and trimmed at both the 5′ and 3′ ends based on a threshold of q30 using cg-pipeline (). passed illumina reads were assembled using spades version 3.1.1 (). this de novo assembly approach yielded 40 large contigs (500 bp each) with an n50 size of 207,332 bp, an average […]

PMCID: 4110763
PMID: 25013135
DOI: 10.1128/genomeA.00617-14

[…] scaffolded using sopra version 1.4.6 to give an assembly size of 3.98 mb, with an n50 of 363 kb (, ). the gene predictions and annotations were performed using the computational genomics pipeline (cg-pipeline) version 0.4 and rast (, ), which predicted and annotated 3,533 coding genes. the g+c content is 47.5%., a phylogeny was constructed based on core genes, and 2012el-1759 was found […]

PMCID: 3705451
PMID: 23820394
DOI: 10.1128/mBio.00398-13

[…] we sequenced, closed, and annotated (). to improve assembly quality, we trimmed poor quality from the ends of reads and removed reads of bad quality using the script run_assembly_trimclean.pl from cg-pipeline (cgp) with default options or with a minimum length of 30 bp and no trimming for the 36-bp read sets (). de novo assembly was performed on resulting reads using cgp, which assembles […]


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CG-Pipeline institution(s)
School of Biology, Georgia Institute of Technology, Atlanta, GA, USA

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