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{ "count": 123, "next": "?page=2", "previous": null, "list": [ { "name": "ntLink", "description": "Toolkit for de novo genome assembly scaffolding and mapping using long reads.", "homepage": "https://github.com/bcgsc/ntLink", "biotoolsID": "ntlink", "biotoolsCURIE": "biotools:ntlink", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3216", "term": "Scaffolding" }, { "uri": "http://edamontology.org/operation_0524", "term": "De-novo assembly" }, { "uri": "http://edamontology.org/operation_0525", "term": "Genome assembly" }, { "uri": "http://edamontology.org/operation_0523", "term": "Mapping assembly" }, { "uri": "http://edamontology.org/operation_3192", "term": "Sequence trimming" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" }, { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" }, { "uri": "http://edamontology.org/topic_3673", "term": "Whole genome sequencing" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/bcgsc/ntLink.git", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1002/CPZ1.733", "pmid": "37039735", "pmcid": "PMC10091225", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "ntLink: A Toolkit for De Novo Genome Assembly Scaffolding and Mapping Using Long Reads", "abstract": "With the increasing affordability and accessibility of genome sequencing data, de novo genome assembly is an important first step to a wide variety of downstream studies and analyses. Therefore, bioinformatics tools that enable the generation of high-quality genome assemblies in a computationally efficient manner are essential. Recent developments in long-read sequencing technologies have greatly benefited genome assembly work, including scaffolding, by providing long-range evidence that can aid in resolving the challenging repetitive regions of complex genomes. ntLink is a flexible and resource-efficient genome scaffolding tool that utilizes long-read sequencing data to improve upon draft genome assemblies built from any sequencing technologies, including the same long reads. Instead of using read alignments to identify candidate joins, ntLink utilizes minimizer-based mappings to infer how input sequences should be ordered and oriented into scaffolds. Recent improvements to ntLink have added important features such as overlap detection, gap-filling, and in-code scaffolding iterations. Here, we present three basic protocols demonstrating how to use each of these new features to yield highly contiguous genome assemblies, while still maintaining ntLink's proven computational efficiency. Further, as we illustrate in the alternate protocols, the lightweight minimizer-based mappings that enable ntLink scaffolding can also be utilized for other downstream applications, such as misassembly detection. With its modularity and multiple modes of execution, ntLink has broad benefit to the genomics community, from genome scaffolding and beyond. ntLink is an open-source project and is freely available from https://github.com/bcgsc/ntLink. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: ntLink scaffolding using overlap detection. Basic Protocol 2: ntLink scaffolding with gap-filling. Basic Protocol 3: Running in-code iterations of ntLink scaffolding. Alternate Protocol 1: Generating long-read to contig mappings with ntLink. Alternate Protocol 2: Using ntLink mappings for genome assembly correction with Tigmint-long. Support Protocol: Installing ntLink.", "date": "2023-04-01T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Coombe L." }, { "name": "Warren R.L." }, { "name": "Wong J." }, { "name": "Nikolic V." }, { "name": "Birol I." } ], "journal": "Current Protocols" } } ], "credit": [ { "name": "Lauren Coombe", "email": "lcoombe@bcgsc.ca", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Inanc Birol", "email": "ibirol@bcgsc.ca", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2023-09-15T16:26:06.061484Z", "lastUpdate": "2023-09-15T16:26:06.064198Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "BRIDGEcereal", "description": "BRIDGEcereal provides a user-friendly interface to efficiently identify large indels from pan-genomes of major cereal crops, accelerating gene discovery for important traits.", "homepage": "https://bridgecereal.scinet.usda.gov", "biotoolsID": "bridgecereal", "biotoolsCURIE": "biotools:bridgecereal", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0452", "term": "Indel detection" }, { "uri": "http://edamontology.org/operation_0310", "term": "Sequence assembly" }, { "uri": "http://edamontology.org/operation_3196", "term": "Genotyping" }, { "uri": "http://edamontology.org/operation_0487", "term": "Haplotype mapping" }, { "uri": "http://edamontology.org/operation_2928", "term": "Alignment" }, { "uri": "http://edamontology.org/operation_0291", "term": "Sequence clustering" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2299", "term": "Gene name" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0872", "term": "Phylogenetic tree" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0865", "term": "Sequence similarity score" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3517", "term": "GWAS study" }, { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/xianranli/CHOICE_CLIPS", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://bridgecereal.scinet.usda.gov/Instruction", "type": [ "Quick start guide" ], "note": null } ], "publication": [ { "doi": "10.1016/j.molp.2023.05.005", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Streamline unsupervised machine learning to survey and graph indel-based haplotypes from pan-genomes", "abstract": "", "date": "2023-06-05T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Zhang B." }, { "name": "Huang H." }, { "name": "Tibbs-Cortes L.E." }, { "name": "Vanous A." }, { "name": "Zhang Z." }, { "name": "Sanguinet K." }, { "name": "Garland-Campbell K.A." }, { "name": "Yu J." }, { "name": "Li X." } ], "journal": "Molecular Plant" } } ], "credit": [ { "name": "Xianran Li", "email": "xianran.li@usda.gov", "url": null, "orcidid": "https://orcid.org/0000-0002-4252-6911", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2023-08-07T17:02:48.364868Z", "lastUpdate": "2023-08-07T17:31:23.486174Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Clustal Omega (EBI)", "description": "Multiple sequence alignment using guide trees and HMM profile-profile techniques.", "homepage": "http://www.ebi.ac.uk/Tools/msa/clustalo/", "biotoolsID": "clustalo_ebi", "biotoolsCURIE": "biotools:clustalo_ebi", "version": [ "1" ], "otherID": [ { "value": "RRID:SCR_001591", "type": "rrid", "version": null } ], "relation": [ { "biotoolsID": "clustalo", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0492", "term": "Multiple sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "clustal", "EBI Tools", "Job Dispatcher Tools" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.ebi.ac.uk/support/", "type": [ "Helpdesk" ], "note": null } ], "download": [ { "url": "http://www.clustal.org/omega/", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "http://www.ebi.ac.uk/about/terms-of-use", "type": [ "Terms of use" ], "note": null }, { "url": "http://www.ebi.ac.uk/Tools/msa/clustalo/", "type": [ "General" ], "note": null }, { "url": "http://www.clustal.org/omega/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1002/0471250953.bi0313s48", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Clustal Omega", "abstract": "Clustal Omega is a package for making multiple sequence alignments of amino acid or nucleotide sequences, quickly and accurately. It is a complete upgrade and rewrite of earlier Clustal programs. This unit describes how to run Clustal Omega interactively from a command line, although it can also be run online from several sites. The unit describes a basic protocol for taking a set of unaligned sequences and producing a full alignment. There are also protocols for using an external HMM or iteration to help improve an alignment.", "date": "2014-01-01T00:00:00Z", "citationCount": 323, "authors": [ { "name": "Sievers F." }, { "name": "Higgins D.G." } ], "journal": "Current Protocols in Bioinformatics" } }, { "doi": "10.1093/nar/gkac240", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Search and sequence analysis tools services from EMBL-EBI in 2022", "abstract": "The EMBL-EBI search and sequence analysis tools frameworks provide integrated access to EMBL-EBI's data resources and core bioinformatics analytical tools. EBI Search (https://www.ebi.ac.uk/ebisearch) provides a full-text search engine across nearly 5 billion entries, while the Job Dispatcher tools framework (https://www.ebi.ac.uk/services) enables the scientific community to perform a diverse range of sequence analysis using popular bioinformatics applications. Both allow users to interact through user-friendly web applications, as well as via RESTful and SOAP-based APIs. Here, we describe recent improvements to these services and updates made to accommodate the increasing data requirements during the COVID-19 pandemic.", "date": "2022-07-05T00:00:00Z", "citationCount": 376, "authors": [ { "name": "Madeira F." }, { "name": "Pearce M." }, { "name": "Tivey A.R.N." }, { "name": "Basutkar P." }, { "name": "Lee J." }, { "name": "Edbali O." }, { "name": "Madhusoodanan N." }, { "name": "Kolesnikov A." }, { "name": "Lopez R." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Des Higgins", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "EMBL-EBI", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "University College Dublin", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Job Dispatcher", "email": null, "url": "https://www.ebi.ac.uk/Tools/jdispatcher", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "jdispatcher", "additionDate": "2015-01-29T15:47:29Z", "lastUpdate": "2023-08-04T09:36:28.961052Z", "editPermission": { "type": "group", "authors": [ "nandana", "biomadeira" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Jalview", "description": "Jalview is a free program for multiple sequence alignment editing, visualisation and analysis. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation.", "homepage": "https://www.jalview.org/", "biotoolsID": "Jalview", "biotoolsCURIE": "biotools:Jalview", "version": [ "2.11.2.7" ], "otherID": [], "relation": [ { "biotoolsID": "jabaws", "type": "uses" }, { "biotoolsID": "chimera", "type": "uses" }, { "biotoolsID": "chimerax", "type": "uses" }, { "biotoolsID": "pymol", "type": "uses" }, { "biotoolsID": "bioconda", "type": "includedIn" }, { "biotoolsID": "3d-beacons", "type": "uses" }, { "biotoolsID": "uniprot", "type": "uses" }, { "biotoolsID": "pfam", "type": "uses" }, { "biotoolsID": "ensembl", "type": "uses" }, { "biotoolsID": "pdb", "type": "uses" }, { "biotoolsID": "rfam", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0564", "term": "Sequence visualisation" }, { "uri": "http://edamontology.org/operation_0324", "term": "Phylogenetic tree analysis" }, { "uri": "http://edamontology.org/operation_3081", "term": "Sequence alignment editing" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1939", "term": "GFF3-seq" }, { "uri": "http://edamontology.org/format_1982", "term": "ClustalW format" }, { "uri": "http://edamontology.org/format_1961", "term": "Stockholm format" }, { "uri": "http://edamontology.org/format_1984", "term": "FASTA-aln" }, { "uri": "http://edamontology.org/format_1938", "term": "GFF2-seq" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1948", "term": "nbrf/pir" }, { "uri": "http://edamontology.org/format_3774", "term": "BioJSON (Jalview)" }, { "uri": "http://edamontology.org/format_1997", "term": "PHYLIP format" }, { "uri": "http://edamontology.org/format_3313", "term": "BLC" }, { "uri": "http://edamontology.org/format_3311", "term": "RNAML" }, { "uri": "http://edamontology.org/format_1947", "term": "GCG MSF" }, { "uri": "http://edamontology.org/format_3015", "term": "Pileup" }, { "uri": "http://edamontology.org/format_1477", "term": "mmCIF" }, { "uri": "http://edamontology.org/format_3016", "term": "VCF" }, { "uri": "http://edamontology.org/format_1915", "term": "Format" } ] }, { "data": { "uri": "http://edamontology.org/data_0886", "term": "Structure alignment" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1948", "term": "nbrf/pir" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_1961", "term": "Stockholm format" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1997", "term": "PHYLIP format" }, { "uri": "http://edamontology.org/format_3313", "term": "BLC" }, { "uri": "http://edamontology.org/format_3774", "term": "BioJSON (Jalview)" }, { "uri": "http://edamontology.org/format_1947", "term": "GCG MSF" }, { "uri": "http://edamontology.org/format_3015", "term": "Pileup" }, { "uri": "http://edamontology.org/format_1982", "term": "ClustalW format" } ] }, { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3603", "term": "PNG" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_3466", "term": "EPS" }, { "uri": "http://edamontology.org/format_3604", "term": "SVG" }, { "uri": "http://edamontology.org/format_1915", "term": "Format" } ] } ], "note": "Other Input formats:\nAMSA (.amsa);\nJnetFile (.concise, .jnet);\nPFAM (.pfam);\nSubstitution matrix (.matrix);\nJalview Project File (.jvp);\nJalview Feature File (.features, .jvfeatures);\nJalview Annotations File (.annotations, .jvannotations);\n\n...\nOther Output formats:\nPFAM (.pfam);\nBioJS (.biojs) (interactive HTML/Javascript);\nJalview Project File (.jvp);", "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "UK" ], "elixirCommunity": [], "link": [ { "url": "https://discourse.jalview.org/", "type": [ "Discussion forum" ], "note": null }, { "url": "https://issues.jalview.org/", "type": [ "Issue tracker" ], "note": null }, { "url": "https://www.jalview.org/development/jalview_develop/", "type": [ "Other" ], "note": "Latest development version" }, { "url": "https://source.jalview.org/crucible/browse/jalview", "type": [ "Repository" ], "note": null }, { "url": "https://twitter.com/Jalview", "type": [ "Social media" ], "note": "Twitter feed" }, { "url": "https://www.youtube.com/channel/UCIjpnvZB770yz7ftbrJ0tfw", "type": [ "Social media" ], "note": "YouTube training videos" } ], "download": [ { "url": "https://www.jalview.org/download", "type": "Downloads page", "note": null, "version": null }, { "url": "https://www.jalview.org/download/source/", "type": "Source code", "note": null, "version": null }, { "url": "https://www.jalview.org/download/?os=all", "type": "Binaries", "note": "Binaries for all platforms", "version": null }, { "url": "https://www.jalview.org/favicon.svg", "type": "Icon", "note": null, "version": null }, { "url": "https://www.jalview.org/download/other/jar/", "type": "Binaries", "note": "Executable JAR file", "version": null } ], "documentation": [ { "url": "https://www.jalview.org/about/citation", "type": [ "Citation instructions" ], "note": null }, { "url": "https://www.jalview.org/training/", "type": [ "Training material" ], "note": "Hands-on exercises, Training courses and Training videos" }, { "url": "https://www.jalview.org/help/faq", "type": [ "FAQ" ], "note": null }, { "url": "https://www.jalview.org/help/documentation/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btp033", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Jalview Version 2-A multiple sequence alignment editor and analysis workbench", "abstract": "Summary: Jalview Version 2 is a system for interactive WYSIWYG editing, analysis and annotation of multiple sequence alignments. Core features include keyboard and mouse-based editing, multiple views and alignment overviews, and linked structure display with Jmol. Jalview 2 is available in two forms: a lightweight Java applet for use in web applications, and a powerful desktop application that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server. © 2009 The Author(s).", "date": "2009-05-07T00:00:00Z", "citationCount": 5999, "authors": [ { "name": "Waterhouse A.M." }, { "name": "Procter J.B." }, { "name": "Martin D.M.A." }, { "name": "Clamp M." }, { "name": "Barton G.J." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Jim Procter", "email": null, "url": "http://www.lifesci.dundee.ac.uk/people/jim-procter", "orcidid": "https://orcid.org/0000-0002-7865-7382", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Geoff Barton", "email": null, "url": "https://www.lifesci.dundee.ac.uk/people/geoff-barton", "orcidid": "https://orcid.org/0000-0002-9014-5355", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "community": null, "owner": "ben_s", "additionDate": "2019-02-13T17:01:40Z", "lastUpdate": "2023-07-22T09:24:44.755337Z", "editPermission": { "type": "group", "authors": [ "ben_s", "jimprocter" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MuGVRE", "description": "The MuG Virtual Research Environment is an analysis platform for 3D/4D genomics analyses. 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Previously, HMMER has mainly been available only as a computationally intensive UNIX command-line tool, restricting its use. Recent advances in the software, HMMER3, have resulted in a 100-fold speed gain relative to previous versions. It is now feasible to make efficient profile hidden Markov model (profile HMM) searches via the web. A HMMER web server (http://hmmer.janelia.org) has been designed and implemented such that most protein database searches return within a few seconds. Methods are available for searching either a single protein sequence, multiple protein sequence alignment or profile HMM against a target sequence database, and for searching a protein sequence against Pfam. The web server is designed to cater to a range of different user expertise and accepts batch uploading of multiple queries at once. All search methods are also available as RESTful web services, thereby allowing them to be readily integrated as remotely executed tasks in locally scripted workflows. 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