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CGAL specifications


Unique identifier OMICS_04066
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Mapped reads to assemblies
Input format SAM
Output data Number of contigs, total likelihood value, likelihood value of reads mapped by the mapping tool, likelihood value corresponding to reads not mapped, total number of paired-end reads, number of reads not mapped by the mapper
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
Computer skills Advanced
Version 0.9.6
Stability Beta
Maintained Yes




No version available

Publication for CGAL

CGAL citations


Adaptation in a Fibronectin Binding Autolysin of Staphylococcus saprophyticus

PMCID: 5705806
PMID: 29202045
DOI: 10.1128/mSphere.00511-17

[…] to compare assemblies from spades (), masurca (), and velvet (). kmergenie () was used to select kmer sizes for assembly. imetamos uses fastqc, quast (), reapr (), lap (), ale (), freebayes (), and cgal () to evaluate the quality of reads and assemblies. we also used kraken () to detect potential contamination in sequence data. for all newly assembled isolates (43, ssc01-05, ssmast), the spades […]


Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes

Microb Genom
PMCID: 5643016
PMID: 29114402
DOI: 10.1099/mgen.0.000123

[…] tool combinations and tables s11 and s12 for gene predictions. our agapes reconstruction – although slightly more fragmented – achieved the best assembly likelihood according to both the lap [] and cgal [] score. the medusa scaffolder was not able to estimate the gap sizes needed as input for gap2seq. hence, the better likelihood in comparison to ragout can be accounted to the missing gaps […]


A molecular portrait of maternal sepsis from Byzantine Troy

PMCID: 5224923
PMID: 28072390
DOI: 10.7554/eLife.20983.043

[…] assembly. imetamos uses fastqc [] to check read data quality. assemblies were evaluated using quast (), reapr (), lap (), ale (), freebayes (), and cgal (). additionally, kraken () was run to detect potential contamination in sequence data. the spades assembly was identified as best for isolates 13, 16, 19, 41, 42, 43, k, m, x, and 129. […]


Approaches for in silico finishing of microbial genome sequences

Genet Mol Biol
PMCID: 5596377
PMID: 28898352
DOI: 10.1590/1678-4685-GMB-2016-0230

[…] the program analyzes the k-mer distribution, c+g% and the relative orientation of the mates (paired-end reads) in the bam file. ale can be obtained from its website, cgal (computing genome assembly likelihood) (): evaluates the accuracy of the assembly using a probability distribution analysis that takes into consideration the expected coverage with that obtained […]


Host Associated Genomic Features of the Novel Uncultured Intracellular Pathogen Ca. Ichthyocystis Revealed by Direct Sequencing of Epitheliocysts

Genome Biol Evol
PMCID: 4943182
PMID: 27190004
DOI: 10.1093/gbe/evw111

[…] spades pipeline () with both single cell and multi-cell modes (). reads were mapped back to the assemblies and genome assembly likelihoods were computed using computing genome assembly likelihood [cgal ()]. for each sample, the assembly with the higher genome assembly likelihood was retained for downstream analysis (supplementary table s1, supplementary material online). ca. ichthyocystis 16s […]


Bayesian Genome Assembly and Assessment by Markov Chain Monte Carlo Sampling

PLoS One
PMCID: 4072599
PMID: 24968249
DOI: 10.1371/journal.pone.0099497

[…] by the same sequence data . recently, several probabilistic approaches have been proposed to quantify assembly certainty and address these limitations. computing genome assembly likelihood (cgal) approximates the likelihood of an assembly given the sequence reads and a generative model learned from the data ; log average probability (lap) approximates the likelihood under a similar […]

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CGAL institution(s)
Department of Electrical Engineering and Computer Sciences, University of California Berkeley, Berkeley, CA, USA; Departments of Mathematics and Molecular & Cell Biology, University of California Berkeley, Berkeley, CA, USA
CGAL funding source(s)
This work was funded by NIH R21 HG006583, Fulbright Science & Technology Fellowship 15093630.

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