Bioinformatic tools wiki

With the advent of single-molecule long-read PacBio sequencing, it is now possible to routinely generate fully closed genome assemblies. To automate this process, we have implemented the UniCycler assembler in an easy-to-use workflow. This assembler provides the advantage of accommodating both short- and long-reads, performing hybrid assembly when both are provided. The tools used for microbial genome assembly have been changing rapidly with the advent of long-read sequencing.

One of the tools which has emerged in this area is Circlator, a tool to take an existing linear genome assembly and turn it into a circular assembly using information from long-read sequencing.

You can refer to the publication and the documentation for more details. Because this tool has a number of dependencies, it may be helpful to use this tool with Nextflow, which executes each step in a Docker container with all of the required dependencies.

The workflow for this tool can be found in this repository , which also has all of the necessary details for running the workflow. Microbial researchers often need to compare multiple genomes in order to identify similarities and differences.

One application of whole-genome shotgun sequencing WGS for microbiome research is the analysis of microbial mixtures on the basis of what microbes are present DNA or are transcriptionally active RNA. To address this analytical need, we developed an analysis tool which takes a set of WGS input data and aligns it against a set of whole microbial genomes. Using just those organisms, the pipeline will then measure the depth of sequencing across all genes for all organisms across all samples, and provide those results to the user in the form of a set of CSV files.

All input files are specified in a single file batchfile. When studying viruses in the human microbiome, one fruitful approach can simply be to perform whole-genome shotgun sequencing WGS and then align all reads against a set of viruses from some reference database.

Think of the monomers as beads or building blocks which, despite having different colors and shapes, all have the same thickness and the same way of connecting to one another. Monomers that can combine in a chain are of the same general class, but each kind of monomer in that class has its own well-defined set of characteristics.

And many monomer molecules can be joined together to form a single, far larger, macromolecule. According to this scheme, the monomers in a given macromolecule of DNA or protein can be treated computationally as letters of an alphabet , put together in pre-programmed arrangements to carry messages or do work in a cell.

The greatest achievement of bioinformatics methods, the Human Genome Project , is practically complete. Because of this the nature and priorities of bioinformatics research and applications have changed. People often talk portentously of our living in the " post-genomic " era. This affects bioinformatics in several ways:. It is worth noting that all of the above post-genomic areas of research depend upon established, pre-genomic sequence analysis techniques.

There are also whole other disciplines of biologically-inspired computation, e. Often these areas interact in strange ways. SigProfiler provides a comprehensive and integrated suite of bioinformatic tools for performing mutational signature analysis. The software covers the analytical lifecycle starting with the generation of the mutational matrix and finishing with signature extraction, as well as supporting functionality for plotting and simulation.

Hover over any of the logos to learn more about each of our software tools, including the GitHub repository, a wiki page describing how to use the tool and the corresponding publication.