NanoporeInspect: An interactive tool for evaluating nanopore sequencing quality and ligation efficiency
In nanopore sequencing, especially in SELEX-based aptamer discovery, the correct ligation of artificial sequences (primers, adapters, barcodes) is crucial for library quality. Errors at this stage can lead to misidentification of sequences and loss of valuable information. Existing quality control t...
Uloženo v:
| Vydáno v: | Journal of bioinformatics and computational biology Ročník 23; číslo 4; s. 2550011 |
|---|---|
| Hlavní autoři: | , , |
| Médium: | Journal Article |
| Jazyk: | angličtina |
| Vydáno: |
Singapore
01.08.2025
|
| Témata: | |
| ISSN: | 1757-6334, 1757-6334 |
| On-line přístup: | Zjistit podrobnosti o přístupu |
| Tagy: |
Přidat tag
Žádné tagy, Buďte první, kdo vytvoří štítek k tomuto záznamu!
|
| Abstract | In nanopore sequencing, especially in SELEX-based aptamer discovery, the correct ligation of artificial sequences (primers, adapters, barcodes) is crucial for library quality. Errors at this stage can lead to misidentification of sequences and loss of valuable information. Existing quality control tools lack focused capabilities to assess the positioning and prevalence of these artificial sequences. NanoporeInspect is a web-based tool designed to fill this gap by providing targeted insights into ligation efficacy and systematic biases within sequencing data. NanoporeInspect operates as a user-friendly, web-based platform that leverages a modern software stack with Flask, Celery and Redis to handle scalable and asynchronous task processing, and Plotly to deliver interactive visualizations. Evaluation of NanoporeInspect on various nanopore datasets demonstrated its effectiveness in discerning differences in ligation quality. Libraries with inefficient ligation showed irregular adapter and barcode distributions, indicating preparation issues, while high-quality libraries displayed uniform patterns, reflecting effective ligation. |
|---|---|
| AbstractList | In nanopore sequencing, especially in SELEX-based aptamer discovery, the correct ligation of artificial sequences (primers, adapters, barcodes) is crucial for library quality. Errors at this stage can lead to misidentification of sequences and loss of valuable information. Existing quality control tools lack focused capabilities to assess the positioning and prevalence of these artificial sequences. NanoporeInspect is a web-based tool designed to fill this gap by providing targeted insights into ligation efficacy and systematic biases within sequencing data. NanoporeInspect operates as a user-friendly, web-based platform that leverages a modern software stack with Flask, Celery and Redis to handle scalable and asynchronous task processing, and Plotly to deliver interactive visualizations. Evaluation of NanoporeInspect on various nanopore datasets demonstrated its effectiveness in discerning differences in ligation quality. Libraries with inefficient ligation showed irregular adapter and barcode distributions, indicating preparation issues, while high-quality libraries displayed uniform patterns, reflecting effective ligation. In nanopore sequencing, especially in SELEX-based aptamer discovery, the correct ligation of artificial sequences (primers, adapters, barcodes) is crucial for library quality. Errors at this stage can lead to misidentification of sequences and loss of valuable information. Existing quality control tools lack focused capabilities to assess the positioning and prevalence of these artificial sequences. NanoporeInspect is a web-based tool designed to fill this gap by providing targeted insights into ligation efficacy and systematic biases within sequencing data. NanoporeInspect operates as a user-friendly, web-based platform that leverages a modern software stack with Flask, Celery and Redis to handle scalable and asynchronous task processing, and Plotly to deliver interactive visualizations. Evaluation of NanoporeInspect on various nanopore datasets demonstrated its effectiveness in discerning differences in ligation quality. Libraries with inefficient ligation showed irregular adapter and barcode distributions, indicating preparation issues, while high-quality libraries displayed uniform patterns, reflecting effective ligation.In nanopore sequencing, especially in SELEX-based aptamer discovery, the correct ligation of artificial sequences (primers, adapters, barcodes) is crucial for library quality. Errors at this stage can lead to misidentification of sequences and loss of valuable information. Existing quality control tools lack focused capabilities to assess the positioning and prevalence of these artificial sequences. NanoporeInspect is a web-based tool designed to fill this gap by providing targeted insights into ligation efficacy and systematic biases within sequencing data. NanoporeInspect operates as a user-friendly, web-based platform that leverages a modern software stack with Flask, Celery and Redis to handle scalable and asynchronous task processing, and Plotly to deliver interactive visualizations. Evaluation of NanoporeInspect on various nanopore datasets demonstrated its effectiveness in discerning differences in ligation quality. Libraries with inefficient ligation showed irregular adapter and barcode distributions, indicating preparation issues, while high-quality libraries displayed uniform patterns, reflecting effective ligation. |
| Author | Khrenova, Maria G Grigoryeva, Maria A Zvereva, Maria I |
| Author_xml | – sequence: 1 givenname: Maria A orcidid: 0000-0002-8851-2187 surname: Grigoryeva fullname: Grigoryeva, Maria A organization: Scientific Research Computing Center, Lomonosov Moscow State University, Leninskie Gory, 1, Building 4, 119234 Moscow, Russian Federation – sequence: 2 givenname: Maria G orcidid: 0000-0001-7117-3089 surname: Khrenova fullname: Khrenova, Maria G organization: Faculty of Chemistry, Lomonosov Moscow State University, Leninskie Gory, Building 1, 119991 Moscow, Russian Federation – sequence: 3 givenname: Maria I orcidid: 0000-0002-7432-1574 surname: Zvereva fullname: Zvereva, Maria I organization: Faculty of Chemistry, Lomonosov Moscow State University, Leninskie Gory, Building 1, 119991 Moscow, Russian Federation |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/40808602$$D View this record in MEDLINE/PubMed |
| BookMark | eNpNkE9LAzEQxYNUtFY_gBfJ0ctq_nY33kqpWih6UM9LNjspgTTZ7mYL_fZGrOBheMPwe8ObuUKTEAMgdEvJA6WCPX4QRlXJCGFSEkJpdYamtJRlMedcTP71F-hSkIpUc8KmaPumQ-xiD-swdGDSE14E7EKCXpvkDoBTjB7b2GM4aD_q5MIWh5MHD7AfIZif2X7U3qUj1qHF3m0zGAMGa51xmTheo3Or_QA3J52hr-fV5_K12Ly_rJeLTWE4E1XBQJWiZJLlcFQKC0bN24orI41UFSG65VYKbWRjgRMOGpRspMj3N5yrtmIzdP-7t-tjzjakeucGA97rAHEcas64EiSXyOjdCR2bHbR117ud7o_133PYN6OMZpE |
| ContentType | Journal Article |
| DBID | CGR CUY CVF ECM EIF NPM 7X8 |
| DOI | 10.1142/S0219720025500118 |
| DatabaseName | Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed MEDLINE - Academic |
| DatabaseTitle | MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) MEDLINE - Academic |
| DatabaseTitleList | MEDLINE MEDLINE - Academic |
| Database_xml | – sequence: 1 dbid: NPM name: PubMed url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 2 dbid: 7X8 name: MEDLINE - Academic url: https://search.proquest.com/medline sourceTypes: Aggregation Database |
| DeliveryMethod | no_fulltext_linktorsrc |
| EISSN | 1757-6334 |
| ExternalDocumentID | 40808602 |
| Genre | Journal Article |
| GroupedDBID | CGR CUY CVF ECM EIF NPM 7X8 |
| ID | FETCH-LOGICAL-c3248-2e9747252602154fec96d839c5c59800ad3f54ac5bfe303eae95b54142b339d82 |
| IEDL.DBID | 7X8 |
| ISICitedReferencesCount | 0 |
| ISICitedReferencesURI | http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=001549422400002&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| ISSN | 1757-6334 |
| IngestDate | Sat Nov 01 15:05:03 EDT 2025 Thu Sep 04 05:03:06 EDT 2025 |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 4 |
| Keywords | nanopore sequencing peak detection ONT primer DNA ligation smoothing distribution barcode quality |
| Language | English |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c3248-2e9747252602154fec96d839c5c59800ad3f54ac5bfe303eae95b54142b339d82 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
| ORCID | 0000-0002-7432-1574 0000-0002-8851-2187 0000-0001-7117-3089 |
| PMID | 40808602 |
| PQID | 3239403944 |
| PQPubID | 23479 |
| ParticipantIDs | proquest_miscellaneous_3239403944 pubmed_primary_40808602 |
| PublicationCentury | 2000 |
| PublicationDate | 2025-Aug 20250801 |
| PublicationDateYYYYMMDD | 2025-08-01 |
| PublicationDate_xml | – month: 08 year: 2025 text: 2025-Aug |
| PublicationDecade | 2020 |
| PublicationPlace | Singapore |
| PublicationPlace_xml | – name: Singapore |
| PublicationTitle | Journal of bioinformatics and computational biology |
| PublicationTitleAlternate | J Bioinform Comput Biol |
| PublicationYear | 2025 |
| Score | 2.3754933 |
| Snippet | In nanopore sequencing, especially in SELEX-based aptamer discovery, the correct ligation of artificial sequences (primers, adapters, barcodes) is crucial for... |
| SourceID | proquest pubmed |
| SourceType | Aggregation Database Index Database |
| StartPage | 2550011 |
| SubjectTerms | Computational Biology - methods Gene Library Internet Nanopore Sequencing - methods Nanopore Sequencing - standards Nanopores Quality Control SELEX Aptamer Technique Sequence Analysis, DNA - methods Software |
| Title | NanoporeInspect: An interactive tool for evaluating nanopore sequencing quality and ligation efficiency |
| URI | https://www.ncbi.nlm.nih.gov/pubmed/40808602 https://www.proquest.com/docview/3239403944 |
| Volume | 23 |
| WOSCitedRecordID | wos001549422400002&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| hasFullText | |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| link | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwpV1LS8QwEA7qevDiA1_riwhey7Zps228iIiLHlwWVNhbSZrpIizp6q4L_ntn0iyeBMFLD4WQMp1kvsxkvo-xK8-BYihRFfd1lOGPjUwsTCRMAqBiWSRQeLGJfDgsxmM1Cgm3ebhWudoT_UZtm4py5L3Ua3hTG-fN7D0i1SiqrgYJjXXWSRHKkFfnY9_9lss86qdpFgqZSSZ6zxjOVC48ivbUZ7-DSh9cBjv__axdth1gJb9t_WCPrYHbZxPcOhvE1_DofEPlNb91nPghfGfUEviiaaYcUStfcX67CXdhDA-XrOld23n5xbWzfOo5ORrHwZNPUOfmAXsd3L_cPURBWCGqED_hygA6RQiJZxmM-FkNlepbREqVrKRCBKltWstMV9LUgCEONChpSC9cmDRVthCHbMM1Do4ZF7EWsUXUEiuD2K_WOANVShNt61wq22WXK7uV6LhUjdAOms95-WO5LjtqjV_OWoaNMkMcS-JYJ38Yfcq2BGny-kt5Z6xT47KFc7ZZLRdv848L7xH4HI6evgEY28FT |
| linkProvider | ProQuest |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=NanoporeInspect%3A+An+interactive+tool+for+evaluating+nanopore+sequencing+quality+and+ligation+efficiency&rft.jtitle=Journal+of+bioinformatics+and+computational+biology&rft.au=Grigoryeva%2C+Maria+A&rft.au=Khrenova%2C+Maria+G&rft.au=Zvereva%2C+Maria+I&rft.date=2025-08-01&rft.issn=1757-6334&rft.eissn=1757-6334&rft.volume=23&rft.issue=4&rft.spage=2550011&rft_id=info:doi/10.1142%2FS0219720025500118&rft.externalDBID=NO_FULL_TEXT |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1757-6334&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1757-6334&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1757-6334&client=summon |