相关论文: Sibelia: A scalable and comprehensive synteny bloc…
We present the phylogeny analysis software SICLE (Sister Clade Extractor), an easy-to-use, high- throughput tool to describe the nearest neighbors to a node of interest in a phylogenetic tree as well as the support value for the…
Motivation: Open-source bacterial genome assembly remains inaccessible to many biologists due to its complexity. Few software solutions exist that are capable of automating all steps in the process of de novo genome assembly from Illumina…
Rapidly assaying the diversity of a bacterial species present in a sample obtained from a hospital patient or an evironmental source has become possible after recent technological advances in DNA sequencing. For several applications it is…
Background: The short reads output by first- and second-generation DNA sequencing instruments cannot completely reconstruct microbial chromosomes. Therefore, most genomes have been left unfinished due to the significant resources required…
Motivation: Working with a large number of genomes simultaneously is of great interest in genetic population and comparative genomics research. Bubbles discovery in multi-genomes coloured de bruijn graph for de novo genome assembly is a…
Microbes are essentially yet convolutedly linked with human lives on the earth. They critically interfere in different physiological processes and thus influence overall health status. Studying microbial species is used to be constrained to…
Assessing the correctness of genome assemblies is an important step in any genome project. Several methods exist, but most are computationally intensive and, in some cases, inappropriate. Here I present baa.pl, a fast and easy-to-use…
Identification of every single genome present in a microbial sample is an important and challenging task with crucial applications. It is challenging because there are typically millions of cells in a microbial sample, the vast majority of…
We present Meraculous2, an update to the Meraculous short-read assembler that includes (1) handling of allelic variation using "bubble" structures within the de Bruijn graph, (2) improved gap closing, and (3) an improved scaffolding…
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…
Motivation: The gene content regulates the biology of an organism. It varies between species and between individuals of the same species. Although tools have been developed to identify gene content changes in bacterial genomes, none is…
One of the most computationally intensive tasks in computational biology is de novo genome assembly, the decoding of the sequence of an unknown genome from redundant and erroneous short sequences. A common assembly paradigm identifies…
Coding information is the main source of heterogeneity (non-randomness) in the sequences of bacterial genomes. This information can be naturally modeled by analysing cluster structures in the "in-phase" triplet distributions of relatively…
PanGeneHome is a web server dedicated to the analysis of available microbial pangenomes. For any prokaryotic taxon with at least three sequenced genomes, PanGeneHome provides (i) conservation level of genes, (ii) pangenome and core-genome…
Motivation: Accurate detection of sequence similarity and homologous recombination are essential parts of many evolutionary analyses. Results: We have developed SimPlot++, an open-source multiplatform application implemented in Python,…
Background: With the rapid growth of massively parallel sequencing technologies, still more laboratories are utilizing sequenced DNA fragments for genomic analyses. Interpretation of sequencing data is, however, strongly dependent on…
We present a new algorithm for identifying superbubbles in HI column density maps of both observed and simulated galaxies that has only a single adjustable parameter. The algorithm includes an automated galaxy-background separation step to…
Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking…
Blini is a tool for quick lookup of nucleotide sequences in databases, and for quick dereplication of sequence collections. It is meant to help clean and characterize large collections of assembled contigs or long sequences that would…
Processing high-throughput DNA sequencing data of individuals or populations requires stringing together independent software tools with many parameters, often leading to non-reproducible pipelines and datasets. We developed grenepipe to…