18,801 research outputs found
Detailed evaluation of data analysis tools for subtyping of bacterial isolates based on whole genome sequencing : Neisseria meningitidis as a proof of concept
Whole genome sequencing is increasingly recognized as the most informative approach for characterization of bacterial isolates. Success of the routine use of this technology in public health laboratories depends on the availability of well-characterized and verified data analysis methods. However, multiple subtyping workflows are now often being used for a single organism, and differences between them are not always well described. Moreover, methodologies for comparison of subtyping workflows, and assessment of their performance are only beginning to emerge. Current work focuses on the detailed comparison of WGS-based subtyping workflows and evaluation of their suitability for the organism and the research context in question. We evaluated the performance of pipelines used for subtyping of Neisseria meningitidis, including the currently widely applied cgMLST approach and different SNP-based methods. In addition, the impact of the use of different tools for detection and filtering of recombinant regions and of different reference genomes were tested. Our benchmarking analysis included both assessment of technical performance of the pipelines and functional comparison of the generated genetic distance matrices and phylogenetic trees. It was carried out using replicate sequencing datasets of high- and low-coverage, consisting mainly of isolates belonging to the clonal complex 269. We demonstrated that cgMLST and some of the SNP-based subtyping workflows showed very good performance characteristics and highly similar genetic distance matrices and phylogenetic trees with isolates belonging to the same clonal complex. However, only two of the tested workflows demonstrated reproducible results for a group of more closely related isolates. Additionally, results of the SNP-based subtyping workflows were to some level dependent on the reference genome used. Interestingly, the use of recombination-filtering software generally reduced the similarity between the gene-by-gene and SNP-based methodologies for subtyping of N. meningitidis. Our study, where N. meningitidis was taken as an example, clearly highlights the need for more benchmarking comparative studies to eventually contribute to a justified use of a specific WGS data analysis workflow within an international public health laboratory context
Recommended from our members
Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads.
As metagenomic studies move to increasing numbers of samples, communities like the human gut may benefit more from the assembly of abundant microbes in many samples, rather than the exhaustive assembly of fewer samples. We term this approach leaderboard metagenome sequencing. To explore protocol optimization for leaderboard metagenomics in real samples, we introduce a benchmark of library prep and sequencing using internal references generated by synthetic long-read technology, allowing us to evaluate high-throughput library preparation methods against gold-standard reference genomes derived from the samples themselves. We introduce a low-cost protocol for high-throughput library preparation and sequencing
OMSim : a simulator for optical map data
Motivation: The Bionano Genomics platform allows for the optical detection of short sequence patterns in very long DNA molecules (up to 2.5 Mbp). Molecules with overlapping patterns can be assembled to generate a consensus optical map of the entire genome. In turn, these optical maps can be used to validate or improve de novo genome assembly projects or to detect large-scale structural variation in genomes. Simulated optical map data can assist in the development and benchmarking of tools that operate on those data, such as alignment and assembly software. Additionally, it can help to optimize the experimental setup for a genome of interest. Such a simulator is currently not available.
Results: We have developed a simulator, OMSim, that produces synthetic optical map data that mimics real Bionano Genomics data. These simulated data have been tested for compatibility with the Bionano Genomics Irys software system and the Irys-scaffolding scripts. OMSim is capable of handling very large genomes (over 30 Gbp) with high throughput and low memory requirements
Essential guidelines for computational method benchmarking
In computational biology and other sciences, researchers are frequently faced
with a choice between several computational methods for performing data
analyses. Benchmarking studies aim to rigorously compare the performance of
different methods using well-characterized benchmark datasets, to determine the
strengths of each method or to provide recommendations regarding suitable
choices of methods for an analysis. However, benchmarking studies must be
carefully designed and implemented to provide accurate, unbiased, and
informative results. Here, we summarize key practical guidelines and
recommendations for performing high-quality benchmarking analyses, based on our
experiences in computational biology.Comment: Minor update
SOAP3-dp: Fast, Accurate and Sensitive GPU-based Short Read Aligner
To tackle the exponentially increasing throughput of Next-Generation
Sequencing (NGS), most of the existing short-read aligners can be configured to
favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging
the computational power of both CPU and GPU with optimized algorithms, delivers
high speed and sensitivity simultaneously. Compared with widely adopted
aligners including BWA, Bowtie2, SeqAlto, GEM and GPU-based aligners including
BarraCUDA and CUSHAW, SOAP3-dp is two to tens of times faster, while
maintaining the highest sensitivity and lowest false discovery rate (FDR) on
Illumina reads with different lengths. Transcending its predecessor SOAP3,
which does not allow gapped alignment, SOAP3-dp by default tolerates alignment
similarity as low as 60 percent. Real data evaluation using human genome
demonstrates SOAP3-dp's power to enable more authentic variants and longer
Indels to be discovered. Fosmid sequencing shows a 9.1 percent FDR on newly
discovered deletions. SOAP3-dp natively supports BAM file format and provides a
scoring scheme same as BWA, which enables it to be integrated into existing
analysis pipelines. SOAP3-dp has been deployed on Amazon-EC2, NIH-Biowulf and
Tianhe-1A.Comment: 21 pages, 6 figures, submitted to PLoS ONE, additional files
available at "https://www.dropbox.com/sh/bhclhxpoiubh371/O5CO_CkXQE".
Comments most welcom
SInC: An accurate and fast error-model based simulator for SNPs, Indels and CNVs coupled with a read generator for short-read sequence data
We report SInC (SNV, Indel and CNV) simulator and read generator, an
open-source tool capable of simulating biological variants taking into account
a platform-specific error model. SInC is capable of simulating and generating
single- and paired-end reads with user-defined insert size with high efficiency
compared to the other existing tools. SInC, due to its multi-threaded
capability during read generation, has a low time footprint. SInC is currently
optimised to work in limited infrastructure setup and can efficiently exploit
the commonly used quad-core desktop architecture to simulate short sequence
reads with deep coverage for large genomes. Sinc can be downloaded from
https://sourceforge.net/projects/sincsimulator/
- …