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For: Tolstoganov I, Bankevich A, Chen Z, Pevzner PA. cloudSPAdes: assembly of synthetic long reads using de Bruijn graphs. Bioinformatics 2020;35:i61-i70. [PMID: 31510642 PMCID: PMC6612831 DOI: 10.1093/bioinformatics/btz349] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
Number Cited by Other Article(s)
1
Ruperao P, Rangan P, Shah T, Sharma V, Rathore A, Mayes S, Pandey MK. Developing pangenomes for large and complex plant genomes and their representation formats. J Adv Res 2025:S2090-1232(25)00071-2. [PMID: 39894347 DOI: 10.1016/j.jare.2025.01.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 01/27/2025] [Accepted: 01/27/2025] [Indexed: 02/04/2025]  Open
2
Fulke AB, Eranezhath S, Raut S, Jadhav HS. Recent toolset of metagenomics for taxonomical and functional annotation of marine associated viruses: A review. REGIONAL STUDIES IN MARINE SCIENCE 2024;77:103728. [DOI: 10.1016/j.rsma.2024.103728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2025]
3
Jiang L, Quail MA, Fraser-Govil J, Wang H, Shi X, Oliver K, Mellado Gomez E, Yang F, Ning Z. The Bioinformatic Applications of Hi-C and Linked Reads. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024;22:qzae048. [PMID: 38905513 PMCID: PMC11580686 DOI: 10.1093/gpbjnl/qzae048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 05/07/2024] [Accepted: 06/19/2024] [Indexed: 06/23/2024]
4
Tolstoganov I, Chen Z, Pevzner P, Korobeynikov A. SpLitteR: diploid genome assembly using TELL-Seq linked-reads and assembly graphs. PeerJ 2024;12:e18050. [PMID: 39351368 PMCID: PMC11441382 DOI: 10.7717/peerj.18050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 08/15/2024] [Indexed: 10/04/2024]  Open
5
Zhang Z, Xiao J, Wang H, Yang C, Huang Y, Yue Z, Chen Y, Han L, Yin K, Lyu A, Fang X, Zhang L. Exploring high-quality microbial genomes by assembling short-reads with long-range connectivity. Nat Commun 2024;15:4631. [PMID: 38821971 PMCID: PMC11143213 DOI: 10.1038/s41467-024-49060-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 05/17/2024] [Indexed: 06/02/2024]  Open
6
Meleshko D, Prjbelski AD, Raiko M, Tomescu AI, Tilgner H, Hajirasouliha I. cloudrnaSPAdes: isoform assembly using bulk barcoded RNA sequencing data. Bioinformatics 2024;40:btad781. [PMID: 38262343 PMCID: PMC10868327 DOI: 10.1093/bioinformatics/btad781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 12/09/2023] [Accepted: 01/18/2024] [Indexed: 01/25/2024]  Open
7
Yang C, Zhang Z, Huang Y, Xie X, Liao H, Xiao J, Veldsman WP, Yin K, Fang X, Zhang L. LRTK: a platform agnostic toolkit for linked-read analysis of both human genome and metagenome. Gigascience 2024;13:giae028. [PMID: 38869148 PMCID: PMC11170215 DOI: 10.1093/gigascience/giae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 03/15/2024] [Accepted: 05/09/2024] [Indexed: 06/14/2024]  Open
8
Naithani S, Deng CH, Sahu SK, Jaiswal P. Exploring Pan-Genomes: An Overview of Resources and Tools for Unraveling Structure, Function, and Evolution of Crop Genes and Genomes. Biomolecules 2023;13:1403. [PMID: 37759803 PMCID: PMC10527062 DOI: 10.3390/biom13091403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/29/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023]  Open
9
Mak L, Meleshko D, Danko DC, Barakzai WN, Maharjan S, Belchikov N, Hajirasouliha I. Ariadne: synthetic long read deconvolution using assembly graphs. Genome Biol 2023;24:197. [PMID: 37641111 PMCID: PMC10463629 DOI: 10.1186/s13059-023-03033-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 08/07/2023] [Indexed: 08/31/2023]  Open
10
Meleshko D, Prjbelski AD, Raiko M, Tomescu AI, Tilgner H, Hajirasouliha I. cloudrnaSPAdes: Isoform assembly using bulk barcoded RNA sequencing data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550587. [PMID: 37546844 PMCID: PMC10402000 DOI: 10.1101/2023.07.25.550587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
11
Baltoumas FA, Karatzas E, Paez-Espino D, Venetsianou NK, Aplakidou E, Oulas A, Finn RD, Ovchinnikov S, Pafilis E, Kyrpides NC, Pavlopoulos GA. Exploring microbial functional biodiversity at the protein family level-From metagenomic sequence reads to annotated protein clusters. FRONTIERS IN BIOINFORMATICS 2023;3:1157956. [PMID: 36959975 PMCID: PMC10029925 DOI: 10.3389/fbinf.2023.1157956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 02/21/2023] [Indexed: 03/06/2023]  Open
12
Qi Y, Gu S, Zhang Y, Guo L, Xu M, Cheng X, Wang O, Sun Y, Chen J, Fang X, Liu X, Deng L, Fan G. MetaTrass: A high-quality metagenome assembler of the human gut microbiome by cobarcoding sequencing reads. IMETA 2022;1:e46. [PMID: 38867906 PMCID: PMC10989976 DOI: 10.1002/imt2.46] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/28/2022] [Accepted: 07/20/2022] [Indexed: 06/14/2024]
13
Faure R, Lavenier D. QuickDeconvolution: fast and scalable deconvolution of linked-read sequencing data. BIOINFORMATICS ADVANCES 2022;2:vbac068. [PMID: 36699389 PMCID: PMC9710601 DOI: 10.1093/bioadv/vbac068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 08/22/2022] [Accepted: 09/21/2022] [Indexed: 01/28/2023]
14
Jiang F, Yang N, Huang H. Characterization and phylogenetic analysis of the mitochondrial genome sequence of Heniochus acuminatus. Mitochondrial DNA B Resour 2022;7:1694-1695. [PMID: 36188664 PMCID: PMC9518272 DOI: 10.1080/23802359.2022.2049016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]  Open
15
Meleshko D, Yang R, Marks P, Williams S, Hajirasouliha I. Efficient detection and assembly of non-reference DNA sequences with synthetic long reads. Nucleic Acids Res 2022;50:e108. [PMID: 35924489 PMCID: PMC9561269 DOI: 10.1093/nar/gkac653] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/10/2022] [Accepted: 08/01/2022] [Indexed: 11/14/2022]  Open
16
Yang C, Chowdhury D, Zhang Z, Cheung WK, Lu A, Bian Z, Zhang L. A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data. Comput Struct Biotechnol J 2021;19:6301-6314. [PMID: 34900140 PMCID: PMC8640167 DOI: 10.1016/j.csbj.2021.11.028] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 12/16/2022]  Open
17
Guo L, Xu M, Wang W, Gu S, Zhao X, Chen F, Wang O, Xu X, Seim I, Fan G, Deng L, Liu X. SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme. BMC Bioinformatics 2021;22:158. [PMID: 33765921 PMCID: PMC7993450 DOI: 10.1186/s12859-021-04081-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 03/16/2021] [Indexed: 12/30/2022]  Open
18
Zhang Z, Liu G, Chen Y, Xue W, Ji Q, Xu Q, Zhang H, Fan G, Huang H, Jiang L, Chen J. Comparison of different sequencing strategies for assembling chromosome-level genomes of extremophiles with variable GC content. iScience 2021;24:102219. [PMID: 33748707 PMCID: PMC7961107 DOI: 10.1016/j.isci.2021.102219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 01/20/2021] [Accepted: 02/18/2021] [Indexed: 01/23/2023]  Open
19
Majidian S, Kahaei MH, de Ridder D. Hap10: reconstructing accurate and long polyploid haplotypes using linked reads. BMC Bioinformatics 2020;21:253. [PMID: 32552661 PMCID: PMC7302376 DOI: 10.1186/s12859-020-03584-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 06/05/2020] [Indexed: 01/23/2023]  Open
20
Chen Z, Pham L, Wu TC, Mo G, Xia Y, Chang PL, Porter D, Phan T, Che H, Tran H, Bansal V, Shaffer J, Belda-Ferre P, Humphrey G, Knight R, Pevzner P, Pham S, Wang Y, Lei M. Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information. Genome Res 2020;30:898-909. [PMID: 32540955 PMCID: PMC7370886 DOI: 10.1101/gr.260380.119] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 06/10/2020] [Indexed: 02/06/2023]
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