In statistics and probability theory, the median is the value separating the higher half from the lower half of a data sample, a population, or a probability distribution. For a data set, it may be thought of as "the middle" value. The basic feature of the median in describing data compared to the mean is that it is not skewed by a small proportion of extremely large or small values, and therefore provides a better representation of the center. Median income, for example, may be a better way to describe center of the income distribution because increases in the largest incomes alone have no effect on median. For this reason, the median is of central importance in robust statistics.
In genetics, shotgun sequencing is a method used for sequencing random DNA strands. It is named by analogy with the rapidly expanding, quasi-random shot grouping of a shotgun.
In statistics, the kth order statistic of a statistical sample is equal to its kth-smallest value. Together with rank statistics, order statistics are among the most fundamental tools in non-parametric statistics and inference.
A contig is a set of overlapping DNA segments that together represent a consensus region of DNA. In bottom-up sequencing projects, a contig refers to overlapping sequence data (reads); in top-down sequencing projects, contig refers to the overlapping clones that form a physical map of the genome that is used to guide sequencing and assembly. Contigs can thus refer both to overlapping DNA sequences and to overlapping physical segments (fragments) contained in clones depending on the context.
In statistics, the Mann–Whitney U test is a nonparametric test of the null hypothesis that, for randomly selected values X and Y from two populations, the probability of X being greater than Y is equal to the probability of Y being greater than X.
In computer science, a selection algorithm is an algorithm for finding the th smallest value in a collection of ordered values, such as numbers. The value that it finds is called the th order statistic. Selection includes as special cases the problems of finding the minimum, median, and maximum element in the collection. Selection algorithms include quickselect, and the median of medians algorithm. When applied to a collection of values, these algorithms take linear time, as expressed using big O notation. For data that is already structured, faster algorithms may be possible; as an extreme case, selection in an already-sorted array takes time .
The Wilcoxon signed-rank test is a non-parametric statistical hypothesis test used either to test the location of a population based on a sample of data, or to compare the locations of two populations using two matched samples. The one-sample version serves a purpose similar to that of the one-sample Student's t-test. For two matched samples, it is a paired difference test like the paired Student's t-test. The Wilcoxon test can be a good alternative to the t-test when population means are not of interest; for example, when one wishes to test whether a population's median is nonzero, or whether there is a better than 50% chance that a sample from one population is greater than a sample from another population.
Synthetic genomics is a nascent field of synthetic biology that uses aspects of genetic modification on pre-existing life forms, or artificial gene synthesis to create new DNA or entire lifeforms.
DNA sequencing theory is the broad body of work that attempts to lay analytical foundations for determining the order of specific nucleotides in a sequence of DNA, otherwise known as DNA sequencing. The practical aspects revolve around designing and optimizing sequencing projects, predicting project performance, troubleshooting experimental results, characterizing factors such as sequence bias and the effects of software processing algorithms, and comparing various sequencing methods to one another. In this sense, it could be considered a branch of systems engineering or operations research. The permanent archive of work is primarily mathematical, although numerical calculations are often conducted for particular problems too. DNA sequencing theory addresses physical processes related to sequencing DNA and should not be confused with theories of analyzing resultant DNA sequences, e.g. sequence alignment. Publications sometimes do not make a careful distinction, but the latter are primarily concerned with algorithmic issues. Sequencing theory is based on elements of mathematics, biology, and systems engineering, so it is highly interdisciplinary. The subject may be studied within the context of computational biology.
Velvet is an algorithm package that has been designed to deal with de novo genome assembly and short read sequencing alignments. This is achieved through the manipulation of de Bruijn graphs for genomic sequence assembly via the removal of errors and the simplification of repeated regions. Velvet has also been implemented in commercial packages, such as Sequencher, Geneious, MacVector and BioNumerics.
RNA-Seq is a technique that uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA molecules in a biological sample, providing a snapshot of gene expression in the sample, also known as transcriptome.
A reference genome is a digital nucleic acid sequence database, assembled by scientists as a representative example of the set of genes in one idealized individual organism of a species. As they are assembled from the sequencing of DNA from a number of individual donors, reference genomes do not accurately represent the set of genes of any single individual organism. Instead, a reference provides a haploid mosaic of different DNA sequences from each donor. For example, one of the most recent human reference genomes, assembly GRCh38/hg38, is derived from >60 genomic clone libraries. There are reference genomes for multiple species of viruses, bacteria, fungus, plants, and animals. Reference genomes are typically used as a guide on which new genomes are built, enabling them to be assembled much more quickly and cheaply than the initial Human Genome Project. Reference genomes can be accessed online at several locations, using dedicated browsers such as Ensembl or UCSC Genome Browser.
In bioinformatics, hybrid genome assembly refers to utilizing various sequencing technologies to achieve the task of assembling a genome from fragmented, sequenced DNA resulting from shotgun sequencing. Genome assembly presents one of the most challenging tasks in genome sequencing as most modern DNA sequencing technologies can only produce reads that are, on average, 25-300 base pairs in length. This is orders of magnitude smaller than the average size of a genome. This assembly is computationally difficult and has some inherent challenges, one of these challenges being that genomes often contain complex tandem repeats of sequences that can be thousands of base pairs in length. These repeats can be long enough that second generation sequencing reads are not long enough to bridge the repeat, and, as such, determining the location of each repeat in the genome can be difficult. Resolving these tandem repeats can be accomplished by utilizing long third generation sequencing reads, such as those obtained using the PacBio RS DNA sequencer. These sequences are, on average, 10,000-15,000 base pairs in length and are long enough to span most repeated regions. Using a hybrid approach to this process can increase the fidelity of assembling tandem repeats by being able to accurately place them along a linear scaffold and make the process more computationally efficient.
De novo transcriptome assembly is the de novo sequence assembly method of creating a transcriptome without the aid of a reference genome.
Scaffolding is a technique used in bioinformatics. It is defined as follows:
Link together a non-contiguous series of genomic sequences into a scaffold, consisting of sequences separated by gaps of known length. The sequences that are linked are typically contiguous sequences corresponding to read overlaps.
In computer science, the median of medians is an approximate median selection algorithm, frequently used to supply a good pivot for an exact selection algorithm, most commonly quickselect, that selects the kth smallest element of an initially unsorted array. Median of medians finds an approximate median in linear time. Using this approximate median as an improved pivot, the worst-case complexity of quickselect reduces from quadratic to linear, which is also the asymptotically optimal worst-case complexity of any selection algorithm. In other words, the median of medians is an approximate median-selection algorithm that helps building an asymptotically optimal, exact general selection algorithm, by producing good pivot elements.
SPAdes is a genome assembly algorithm which was designed for single cell and multi-cells bacterial data sets. Therefore, it might not be suitable for large genomes projects.
De novo sequence assemblers are a type of program that assembles short nucleotide sequences into longer ones without the use of a reference genome. These are most commonly used in bioinformatic studies to assemble genomes or transcriptomes. Two common types of de novo assemblers are greedy algorithm assemblers and De Bruijn graph assemblers.
A plant genome assembly represents the complete genomic sequence of a plant species, which is assembled into chromosomes and other organelles by using DNA fragments that are obtained from different types of sequencing technology.
