<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/34877? https://bioinformaticsonline.com/bookmarks/view/36590/digest-in-silico-restriction-digest-of-complete-genomes Mon, 14 May 2018 04:02:52 -0500 https://bioinformaticsonline.com/bookmarks/view/36590/digest-in-silico-restriction-digest-of-complete-genomes <![CDATA[Digest: In silico restriction digest of complete genomes]]> This tool allows to retrieve number of cleavages yielded by commercially available endonucleases in up-to-date sequenced prokaryotic genomes. When the number of fragments is bellow 50, Pulse Field gel Electrophoresis (PFGE) is simulated.

A tool for restriction digest of longuser's sequences is available.

 

Address of the bookmark: http://insilico.ehu.es/digest/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/44561/bactopia-a-flexible-pipeline-for-complete-analysis-of-bacterial-genomes Sat, 08 Jun 2024 16:25:08 -0500 https://bioinformaticsonline.com/bookmarks/view/44561/bactopia-a-flexible-pipeline-for-complete-analysis-of-bacterial-genomes <![CDATA[Bactopia: a flexible pipeline for complete analysis of bacterial genomes]]> Bactopia is a flexible pipeline for complete analysis of bacterial genomes. The goal of Bactopia is process your data with a broad set of tools, so that you can get to the fun part of analyses quicker!

Bactopia was inspired by Staphopia, a workflow we (Tim Read and myself) released that is targeted towards Staphylococcus aureus genomes. Using what we learned from Staphopia and user feedback, Bactopia was developed from scratch with usability, portability, and speed in mind from the start.

Bactopia uses Nextflow to manage the workflow, allowing for support of many types of environments (e.g. cluster or cloud). Bactopia allows for the usage of many public datasets as well as your own datasets to further enhance the analysis of your sequencing. Bactopia only uses software packages available from Bioconda and Conda-Forge to make installation as simple as possible for all users.

To highlight the use of Bactopia and Bactopia Tools, we performed an analysis of 1,664 public Lactobacillus genomes, focusing on Lactobacillus crispatus, a species that is a common part of the human vaginal microbiome. The results from this analysis are published in mSystems under the title: Bactopia: a flexible pipeline for complete analysis of bacterial genomes

Bactopia Workflow

Address of the bookmark: https://bactopia.github.io/latest/

]]> Abhi https://bioinformaticsonline.com/bookmarks/view/38055/ancestral-genomes-a-resource-for-reconstructed-ancestral-genes-and-genomes-across-the-tree-of-life Fri, 02 Nov 2018 08:16:27 -0500 https://bioinformaticsonline.com/bookmarks/view/38055/ancestral-genomes-a-resource-for-reconstructed-ancestral-genes-and-genomes-across-the-tree-of-life <![CDATA[Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life]]>  Ancestral Genomes (http://ancestralgenomes.org) is a resource for comprehensive reconstructions of these ‘fossil genomes’. Comprehensive sets of protein-coding genes have been reconstructed for 78 genomes of now-extinct species that were the common ancestors of extant species from across the tree of life. 

Address of the bookmark: http://ancestralgenomes.org/

]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/36736/checkmassessing-the-quality-of-microbial-genomes-recovered-from-isolates-single-cells-and-metagenomes Wed, 23 May 2018 04:39:26 -0500 https://bioinformaticsonline.com/bookmarks/view/36736/checkmassessing-the-quality-of-microbial-genomes-recovered-from-isolates-single-cells-and-metagenomes <![CDATA[CheckM:Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes]]> CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. It provides robust estimates of genome completeness and contamination by using collocated sets of genes that are ubiquitous and single-copy within a phylogenetic lineage. Assessment of genome quality can also be examined using plots depicting key genomic characteristics (e.g., GC, coding density) which highlight sequences outside the expected distributions of a typical genome. CheckM also provides tools for identifying genome bins that are likely candidates for merging based on marker set compatibility, similarity in genomic characteristics, and proximity within a reference genome tree.

Address of the bookmark: http://ecogenomics.github.io/CheckM/

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/44539/bactopia-a-flexible-pipeline-for-complete-analysis-of-bacterial-genomes Wed, 15 May 2024 14:36:12 -0500 https://bioinformaticsonline.com/bookmarks/view/44539/bactopia-a-flexible-pipeline-for-complete-analysis-of-bacterial-genomes <![CDATA[Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes]]> Bactopia is a flexible pipeline for complete analysis of bacterial genomes. The goal of Bactopia is to process your data with a broad set of tools, so that you can get to the fun part of analyses quicker!

Bactopia can be split into two main parts: Bactopia Analysis Pipeline, and Bactopia Tools.

Bactopia Analysis Pipeline is the main per-isolate workflow in Bactopia. Built with Nextflow, input FASTQs (local or available from SRA/ENA) are put through numerous analyses including: quality control, assembly, annotation, minmer sketch queries, sequence typing, and more.

Bactopia Overview

Bactopia Tools are a set a independent workflows fo

Address of the bookmark: https://github.com/bactopia/bactopia

]]> Abhi https://bioinformaticsonline.com/videolist/watch/2699/translational-bioinformatics-transforming-300-billion-points-of-data Tue, 20 Aug 2013 19:03:47 -0500 https://bioinformaticsonline.com/videolist/watch/2699/translational-bioinformatics-transforming-300-billion-points-of-data <![CDATA[Translational Bioinformatics: Transforming 300 Billion Points of Data]]> Translational Bioinformatics: Transforming 300 Billion Points of Data into Diagnostics, Therapeutics, and New Insights into Disease Air date: Wednesday, June 20, 2012, 3:00:00 PM Time displayed is Eastern Time, Washington DC Local Description: There is an urgent need to translate genome-era discoveries into clinical utility, but the difficulties in making bench-to-bedside translations haven't been well described. The nascent field of translational bioinformatics may help. Dr. Butte's lab at Stanford University builds and applies tools that convert more than 300 billion points of molecular, clinical, and epidemiological data (measured by researchers and clinicians over the past decade) into diagnostics, therapeutics, and new insights into disease. Dr. Butte, a bioinformatician and pediatric endocrinologist, will highlight his lab's work on using publicly available molecular measurements to find new uses for drugs, discovering new treatable mechanisms of disease in type 2 diabetes, and evaluating patients presenting with whole genomes sequenced. The NIH Wednesday Afternoon Lecture Series includes weekly scientific talks by some of the top researchers in the biomedical sciences worldwide. For more information, visit: The NIH Director's Wednesday Afternoon Lecture Series Author: Atul Butte, M.D., Ph.D., Stanford University Runtime: 01:07:42 Permanent link: http://videocast.nih.gov/launch.asp?17321]]> https://bioinformaticsonline.com/bookmarks/view/32851/anges-reconstructing-ancestral-genomes-maps Thu, 18 May 2017 05:27:08 -0500 https://bioinformaticsonline.com/bookmarks/view/32851/anges-reconstructing-ancestral-genomes-maps <![CDATA[ANGES: reconstructing ANcestral GEnomeS maps]]> This page contains the software ANGES 1.01, that aims at reconstucting ancestral genome maps from homologous markers in extant related genomes.

Download

Address of the bookmark: http://paleogenomics.irmacs.sfu.ca/ANGES/

]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/34718/dipspades-assembler-for-highly-polymorphic-diploid-genomes Wed, 20 Dec 2017 18:35:16 -0600 https://bioinformaticsonline.com/bookmarks/view/34718/dipspades-assembler-for-highly-polymorphic-diploid-genomes <![CDATA[dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes.]]> While the number of sequenced diploid genomes have been steadily increasing in the last few years, assembly of highly polymorphic (HP) diploid genomes remains challenging. As a result, there is a shortage of tools for assembling HP genomes from the next generation sequencing (NGS) data. The initial approaches to assembling HP genomes were proposed in the pre-NGS era and are not well suited for NGS projects. To address this limitation, we developed the first de Bruijn graph assembler, dipSPAdes, for HP genomes that significantly improves on the state-of-the-art assemblers for HP diploid genomes.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pubmed/25734602

]]> Jit https://bioinformaticsonline.com/bookmarks/view/36905/d-genies-a-tool-for-dotplot-large-genomes-in-an-interactive-efficient-and-simple-way Mon, 11 Jun 2018 09:41:22 -0500 https://bioinformaticsonline.com/bookmarks/view/36905/d-genies-a-tool-for-dotplot-large-genomes-in-an-interactive-efficient-and-simple-way <![CDATA[D-GENIES: A tool for Dotplot large Genomes in an Interactive, Efficient and Simple way]]> Address of the bookmark: http://dgenies.toulouse.inra.fr/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/44599/p10k-the-protist-10000-genomes Sat, 06 Jul 2024 08:29:30 -0500 https://bioinformaticsonline.com/bookmarks/view/44599/p10k-the-protist-10000-genomes <![CDATA[P10K: The Protist 10,000 Genomes]]> The Protist 10,000 Genomes (P10K) Project aims to decipher the genome sequences and construct a comprehensive database resource containing over 10,000 species of protists, encompassing representatives from every major clade. Samples were collected from diverse habitats, and the genome information was acquired through de novo sequencing, genome re-annotation, and integration of publicly available data. Serving as a centralized data portal for the project, the P10K database primarily focuses on delivering high-quality curation and facilitating efficient retrieval of protist genome data.

Address of the bookmark: https://ngdc.cncb.ac.cn/p10k/

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