PlasCAT: Plasmid Cloud Assembly Tool
Abstract Summary PlasCAT (Plasmid Cloud Assembly Tool) is an easy-to-use cloud-based bioinformatics tool that enables de novo plasmid sequence assembly from raw sequencing data. Nontechnical users can now assemble sequences from long reads and short reads without ever touching a line of code. PlasCA...
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| Veröffentlicht in: | Bioinformatics (Oxford, England) England), 2024-05, Vol.40 (5) |
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| container_title | Bioinformatics (Oxford, England) |
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| creator | Peccoud, Samuel Berezin, Casey-Tyler Hernandez, Sarah I Peccoud, Jean |
| description | Abstract
Summary
PlasCAT (Plasmid Cloud Assembly Tool) is an easy-to-use cloud-based bioinformatics tool that enables de novo plasmid sequence assembly from raw sequencing data. Nontechnical users can now assemble sequences from long reads and short reads without ever touching a line of code. PlasCAT uses high-performance computing servers to reduce run times on assemblies and deliver results faster.
Availability and implementation
PlasCAT is freely available on the web at https://sequencing.genofab.com. The assembly pipeline source code and server code are available for download at https://bitbucket.org/genofabinc/workspace/projects/PLASCAT. Click the Cancel button to access the source code without authenticating. Web servers implemented in React.js and Python, with all major browsers supported. |
| doi_str_mv | 10.1093/bioinformatics/btae299 |
| format | Article |
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Summary
PlasCAT (Plasmid Cloud Assembly Tool) is an easy-to-use cloud-based bioinformatics tool that enables de novo plasmid sequence assembly from raw sequencing data. Nontechnical users can now assemble sequences from long reads and short reads without ever touching a line of code. PlasCAT uses high-performance computing servers to reduce run times on assemblies and deliver results faster.
Availability and implementation
PlasCAT is freely available on the web at https://sequencing.genofab.com. The assembly pipeline source code and server code are available for download at https://bitbucket.org/genofabinc/workspace/projects/PLASCAT. Click the Cancel button to access the source code without authenticating. Web servers implemented in React.js and Python, with all major browsers supported.</description><identifier>ISSN: 1367-4811</identifier><identifier>ISSN: 1367-4803</identifier><identifier>EISSN: 1367-4811</identifier><identifier>DOI: 10.1093/bioinformatics/btae299</identifier><identifier>PMID: 38696761</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Applications Note ; Assembly ; Availability ; Bioinformatics ; Cloud Computing ; Computational Biology - methods ; Internet ; Plasmids - genetics ; Sequence Analysis, DNA - methods ; Servers ; Software ; Source code</subject><ispartof>Bioinformatics (Oxford, England), 2024-05, Vol.40 (5)</ispartof><rights>The Author(s) 2024. Published by Oxford University Press. 2024</rights><rights>The Author(s) 2024. Published by Oxford University Press.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c432t-4b398bddf2844e6c4601586bf588c74d81ee9a013b1320abd8e959d4b192e4053</cites><orcidid>0000-0001-7649-6127</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC11101281/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC11101281/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,1598,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38696761$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Peccoud, Samuel</creatorcontrib><creatorcontrib>Berezin, Casey-Tyler</creatorcontrib><creatorcontrib>Hernandez, Sarah I</creatorcontrib><creatorcontrib>Peccoud, Jean</creatorcontrib><title>PlasCAT: Plasmid Cloud Assembly Tool</title><title>Bioinformatics (Oxford, England)</title><addtitle>Bioinformatics</addtitle><description>Abstract
Summary
PlasCAT (Plasmid Cloud Assembly Tool) is an easy-to-use cloud-based bioinformatics tool that enables de novo plasmid sequence assembly from raw sequencing data. Nontechnical users can now assemble sequences from long reads and short reads without ever touching a line of code. PlasCAT uses high-performance computing servers to reduce run times on assemblies and deliver results faster.
Availability and implementation
PlasCAT is freely available on the web at https://sequencing.genofab.com. The assembly pipeline source code and server code are available for download at https://bitbucket.org/genofabinc/workspace/projects/PLASCAT. Click the Cancel button to access the source code without authenticating. 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Berezin, Casey-Tyler ; Hernandez, Sarah I ; Peccoud, Jean</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c432t-4b398bddf2844e6c4601586bf588c74d81ee9a013b1320abd8e959d4b192e4053</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Applications Note</topic><topic>Assembly</topic><topic>Availability</topic><topic>Bioinformatics</topic><topic>Cloud Computing</topic><topic>Computational Biology - methods</topic><topic>Internet</topic><topic>Plasmids - genetics</topic><topic>Sequence Analysis, DNA - methods</topic><topic>Servers</topic><topic>Software</topic><topic>Source code</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Peccoud, Samuel</creatorcontrib><creatorcontrib>Berezin, Casey-Tyler</creatorcontrib><creatorcontrib>Hernandez, Sarah I</creatorcontrib><creatorcontrib>Peccoud, Jean</creatorcontrib><collection>Oxford Journals Open Access Collection</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Aluminium Industry Abstracts</collection><collection>Biotechnology Research Abstracts</collection><collection>Ceramic Abstracts</collection><collection>Computer and Information Systems Abstracts</collection><collection>Corrosion Abstracts</collection><collection>Electronics & Communications Abstracts</collection><collection>Engineered Materials Abstracts</collection><collection>Materials Business File</collection><collection>Mechanical & Transportation Engineering Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Oncogenes and Growth Factors Abstracts</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>METADEX</collection><collection>Technology Research Database</collection><collection>ANTE: Abstracts in New Technology & Engineering</collection><collection>Engineering Research Database</collection><collection>Aerospace Database</collection><collection>Copper Technical Reference Library</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Materials Research Database</collection><collection>ProQuest Computer Science Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Civil Engineering Abstracts</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>Computer and Information Systems Abstracts Academic</collection><collection>Computer and Information Systems Abstracts Professional</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Bioinformatics (Oxford, England)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Peccoud, Samuel</au><au>Berezin, Casey-Tyler</au><au>Hernandez, Sarah I</au><au>Peccoud, Jean</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>PlasCAT: Plasmid Cloud Assembly Tool</atitle><jtitle>Bioinformatics (Oxford, England)</jtitle><addtitle>Bioinformatics</addtitle><date>2024-05-02</date><risdate>2024</risdate><volume>40</volume><issue>5</issue><issn>1367-4811</issn><issn>1367-4803</issn><eissn>1367-4811</eissn><abstract>Abstract
Summary
PlasCAT (Plasmid Cloud Assembly Tool) is an easy-to-use cloud-based bioinformatics tool that enables de novo plasmid sequence assembly from raw sequencing data. Nontechnical users can now assemble sequences from long reads and short reads without ever touching a line of code. PlasCAT uses high-performance computing servers to reduce run times on assemblies and deliver results faster.
Availability and implementation
PlasCAT is freely available on the web at https://sequencing.genofab.com. The assembly pipeline source code and server code are available for download at https://bitbucket.org/genofabinc/workspace/projects/PLASCAT. Click the Cancel button to access the source code without authenticating. Web servers implemented in React.js and Python, with all major browsers supported.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>38696761</pmid><doi>10.1093/bioinformatics/btae299</doi><orcidid>https://orcid.org/0000-0001-7649-6127</orcidid><oa>free_for_read</oa></addata></record> |
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| language | eng |
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| source | Oxford Journals Open Access Collection; MEDLINE; DOAJ Directory of Open Access Journals; EZB-FREE-00999 freely available EZB journals; PubMed Central; Alma/SFX Local Collection |
| subjects | Applications Note Assembly Availability Bioinformatics Cloud Computing Computational Biology - methods Internet Plasmids - genetics Sequence Analysis, DNA - methods Servers Software Source code |
| title | PlasCAT: Plasmid Cloud Assembly Tool |
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