Tool stats & trends
Looking to identify usage trends or leading experts?
|Interface||Command line interface|
|Restrictions to use||None|
|Input data||Mapped reads to assemblies|
|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|
No version available
Publication for CGAL
Adaptation in a Fibronectin Binding Autolysin of Staphylococcus saprophyticus
[…] e 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
[…] l 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 chara […]
A molecular portrait of maternal sepsis from Byzantine Troy
[…] or assembly. iMetAMOS uses FastQC [www.bioinformatics.babraham.ac.uk/projects/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. The MaSur […]
Approaches for in silico finishing of microbial genome sequences
[…] assembly, 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 http://www.alescore.org.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
[…] he 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 r […]
Environmental marine pathogen isolation using mesocosm culture of sharpsnout seabream: striking genomic and morphological features of novel Endozoicomonas sp.
[…] es v 3.1.0 under default settings, which includes read error correction. Assemblies were tested using various K-mers in both single-cell mode and multi-cell mode and quality assessed using QUAST and CGAL (). Single-cell mode produced better assemblies than multi-cell mode, giving 62 776 scaffolds comprising 39.3 Mb. Each scaffold was screened against the NCBInr database using blastx and screened […]
Looking to check out a full list of citations?
Be the first to review CGAL