<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/43801?offset=220 https://bioinformaticsonline.com/bookmarks/view/38598/zenbu-a-collaborative-omics-data-integration-and-interactive-visualization-system Fri, 04 Jan 2019 13:35:26 -0600 https://bioinformaticsonline.com/bookmarks/view/38598/zenbu-a-collaborative-omics-data-integration-and-interactive-visualization-system <![CDATA[ZENBU: a collaborative, omics data integration and interactive visualization system]]> ZENBU is a data integration, data analysis, and visualization system enhanced for RNAseq, ChipSeq, CAGE and other types of next-generation-sequence-tag (NGS) based data. ZENBU allows for novel data exploration through "on-demand" data processing and interactive linked-visualizations and is able to make many-views from the same primary sequence alignment data which users can uploaded from BAM, BED, GFF and tab-text files. 
Please check our documentation wiki for details on how to use the system, or check out some of the views above.

Address of the bookmark: http://fantom.gsc.riken.jp/zenbu/

]]> BioJoker https://bioinformaticsonline.com/bookmarks/view/39200/omtools-a-software-package-for-visualizing-and-processing-optical-mapping-data Fri, 29 Mar 2019 01:21:54 -0500 https://bioinformaticsonline.com/bookmarks/view/39200/omtools-a-software-package-for-visualizing-and-processing-optical-mapping-data <![CDATA[OMTools: a software package for visualizing and processing optical mapping data]]> OMTools, an efficient and intuitive data processing and visualization suite to handle and explore large-scale optical mapping profiles. OMTools includes modules for visualization (OMView), data processing and simulation. These modules together form an accessible and convenient pipeline for optical mapping analyses.

https://github.com/TF-Chan-Lab/OMTools

Address of the bookmark: https://github.com/TF-Chan-Lab/OMTools

]]> BioJoker https://bioinformaticsonline.com/bookmarks/view/41148/pbmm2a-minimap2-frontend-for-pacbio-native-data-formats Tue, 18 Feb 2020 03:36:22 -0600 https://bioinformaticsonline.com/bookmarks/view/41148/pbmm2a-minimap2-frontend-for-pacbio-native-data-formats <![CDATA[pbmm2:A minimap2 frontend for PacBio native data formats]]> pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR.

Address of the bookmark: https://github.com/PacificBiosciences/pbmm2

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/44313/orthovenn3-an-integrated-platform-for-exploring-and-visualizing-orthologous-data-across-genomes Tue, 02 May 2023 00:48:28 -0500 https://bioinformaticsonline.com/bookmarks/view/44313/orthovenn3-an-integrated-platform-for-exploring-and-visualizing-orthologous-data-across-genomes <![CDATA[OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes]]> OrthoVenn3 is a powerful tool for comparative genomics analysis, used as a web server for full genome comparisons, annotation, and evolutionary analysis of orthologous clusters across multiple species. It has already been used by thousands of users from over 60 countries.

Address of the bookmark: https://orthovenn3.bioinfotoolkits.net/

]]> Abhi https://bioinformaticsonline.com/bookmarks/view/44581/biokit-a-set-of-tools-dedicated-to-bioinformatics-data-visualisation Tue, 18 Jun 2024 02:04:39 -0500 https://bioinformaticsonline.com/bookmarks/view/44581/biokit-a-set-of-tools-dedicated-to-bioinformatics-data-visualisation <![CDATA[BioKit: a set of tools dedicated to bioinformatics, data visualisation]]> BioKit is a set of tools dedicated to bioinformatics, data visualisation (biokit.viz), access to online biological data (e.g. UniProt, NCBI thanks to bioservices). It also contains more advanced tools related to data analysis (e.g., biokit.stats). Since R is quite common in bioinformatics, we also provide a convenient module to run R inside your Python scripts or shell (:mod:biokit.rtools module).

Address of the bookmark: https://biokit.readthedocs.io/en/latest/index.html

]]> Neel https://bioinformaticsonline.com/bookmarks/view/44873/bakrep-denglish-blend-of-bakterien-repository-simplifies-access-to-this-data Wed, 13 Aug 2025 02:31:28 -0500 https://bioinformaticsonline.com/bookmarks/view/44873/bakrep-denglish-blend-of-bakterien-repository-simplifies-access-to-this-data <![CDATA[BakRep (Denglish blend of Bakterien & Repository) simplifies access to this data]]> 2,438,386 bacterial genomes at your fingertips consistently processed & characterized, enriched with metadata, accessible via a flexible search engine.

BakRep (Denglish blend of Bakterien & Repository) simplifies access to this data. It integrates enriched genomic information with metadata accessible via a flexible search-engine.

Key features

  • Assembly statistics: ensure data quality with genome-based key metrics
  • Taxonomic classification: robust, purely genome-based classifications (GTDB)
  • MLST: subtyping for deeper insights into genetic variation
  • Annotation: comprehensive & taxonomy-independent (Bakta)
  • Metadata: full original submission records
 

Address of the bookmark: https://bakrep.computational.bio/

]]> Neel https://bioinformaticsonline.com/bookmarks/view/26729/ga4gh-data-working-group Sun, 20 Mar 2016 23:13:07 -0500 https://bioinformaticsonline.com/bookmarks/view/26729/ga4gh-data-working-group <![CDATA[GA4GH Data Working Group]]> GA4GH Data Working Group

Led by David Haussler (UCSC) and Richard Durbin (Sanger Institute), the Data Working Group (DWG) of the Global Alliance brings together the leading Genome Institutes and Centers with IT industry leaders to create global standards and tools for the secure, privacy respecting and interoperable sharing of Genomic data.

More at http://ga4gh.org/#/

Address of the bookmark: http://ga4gh.org/#/

]]> Jitendra Prajapati https://bioinformaticsonline.com/bookmarks/view/37993/platypus-a-haplotype-based-variant-caller-for-next-generation-sequence-data Thu, 25 Oct 2018 06:14:55 -0500 https://bioinformaticsonline.com/bookmarks/view/37993/platypus-a-haplotype-based-variant-caller-for-next-generation-sequence-data <![CDATA[Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data]]> Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly it achieves both high sensitivity and high specificity. Platypus can detect SNPs, MNPs, short indels, replacements and (using the assembly option) deletions up to several kb. It has been extensively tested on whole-genome, exon-capture, and targeted capture data, it has been run on very large datasets as part of the Thousand Genomes and WGS500 projects, and is being used in clinical sequencing trials in the Mainstreaming Cancer Genetics programme. 

Tutorial https://github.com/andyrimmer/Platypus/blob/master/misc/README.txt

Address of the bookmark: http://www.well.ox.ac.uk/platypus

]]> Shruti Paniwala https://bioinformaticsonline.com/news/view/42324/comparative-genomics-data-set-including-240-mammals-released Thu, 19 Nov 2020 06:45:39 -0600 https://bioinformaticsonline.com/news/view/42324/comparative-genomics-data-set-including-240-mammals-released <![CDATA[Comparative Genomics Data Set Including 240 Mammals Released !]]> The genome of 130 mammals was sequenced by a large international consortium and the data was analyzed together with 110 existing genomes to allow scientists to identify the important positions in the DNA. This report, published in Nature today will help advance research on human disease mutations and inform how best to protect endangered species.

In addition to the knowledge of the human genome, all these genomes, widely sampled across mammals, can be used to research how particular organisms respond to different conditions. Some otters, for example, have a thick, water-resistant shell, and some rodents, but not all, have adapted to hibernation. These animal traits will help us to understand human traits, such as metabolic diseases.

image

With climate change and more animal ecosystems being threatened by human activity, the protection of endangered species is becoming increasingly important. Scientists have historically researched several people in various populations of a species to understand the genetic variation that occurs in that species. This is important for understanding how particular species can be protected. In this study, animals on the Red List of Endangered Species of the International Union for Conservation of Nature had fewer differences in their genomes, which is consistent with their endangered status.

Ref @ A comparative genomics multitool for scientific discovery and conservation https://www.nature.com/articles/s41586-020-2876-6

 Data at http://zoonomiaproject.org/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/44545/amr-database Tue, 04 Jun 2024 13:37:21 -0500 https://bioinformaticsonline.com/bookmarks/view/44545/amr-database <![CDATA[AMR Database !]]>
  • ARG-ANNOT. PMID: 24145532
  • CARD. PMID: 23650175
  • MEGARes PMID: 27899569
  • NCBI BioProject: PRJNA313047
  • plasmidfinder PMID: 24777092
  • resfinder. PMID: 22782487
  • VFDB. PMID: 26578559
  • SRST2's version of ARG-ANNOT. PMID: 25422674.
  • VirulenceFinder PMID: 24574290.

    • Address of the bookmark: https://github.com/sanger-pathogens/ariba/wiki/Task%3A-getref

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