185 related articles for article (PubMed ID: 37587527)
1. High-resolution strain-level microbiome composition analysis from short reads.
Liao H; Ji Y; Sun Y
Microbiome; 2023 Aug; 11(1):183. PubMed ID: 37587527
[TBL] [Abstract][Full Text] [Related]
2. MinION™ nanopore sequencing of environmental metagenomes: a synthetic approach.
Brown BL; Watson M; Minot SS; Rivera MC; Franklin RB
Gigascience; 2017 Mar; 6(3):1-10. PubMed ID: 28327976
[TBL] [Abstract][Full Text] [Related]
3. MetaBCC-LR: metagenomics binning by coverage and composition for long reads.
Wickramarachchi A; Mallawaarachchi V; Rajan V; Lin Y
Bioinformatics; 2020 Jul; 36(Suppl_1):i3-i11. PubMed ID: 32657364
[TBL] [Abstract][Full Text] [Related]
4. K2Mem: Discovering Discriminative K-mers From Sequencing Data for Metagenomic Reads Classification.
Storato D; Comin M
IEEE/ACM Trans Comput Biol Bioinform; 2022; 19(1):220-229. PubMed ID: 34606462
[TBL] [Abstract][Full Text] [Related]
5. STEMSIM: a simulator of within-strain short-term evolutionary mutations for longitudinal metagenomic data.
Zhou B; Li H
Bioinformatics; 2023 May; 39(5):. PubMed ID: 37154701
[TBL] [Abstract][Full Text] [Related]
6. StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities.
van Dijk LR; Walker BJ; Straub TJ; Worby CJ; Grote A; Schreiber HL; Anyansi C; Pickering AJ; Hultgren SJ; Manson AL; Abeel T; Earl AM
Genome Biol; 2022 Mar; 23(1):74. PubMed ID: 35255937
[TBL] [Abstract][Full Text] [Related]
7. StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees.
Roosaare M; Vaher M; Kaplinski L; Möls M; Andreson R; Lepamets M; Kõressaar T; Naaber P; Kõljalg S; Remm M
PeerJ; 2017; 5():e3353. PubMed ID: 28533988
[TBL] [Abstract][Full Text] [Related]
8. Recovery of strain-resolved genomes from human microbiome through an integration framework of single-cell genomics and metagenomics.
Arikawa K; Ide K; Kogawa M; Saeki T; Yoda T; Endoh T; Matsuhashi A; Takeyama H; Hosokawa M
Microbiome; 2021 Oct; 9(1):202. PubMed ID: 34641955
[TBL] [Abstract][Full Text] [Related]
9. Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps.
Dilthey AT; Jain C; Koren S; Phillippy AM
Nat Commun; 2019 Jul; 10(1):3066. PubMed ID: 31296857
[TBL] [Abstract][Full Text] [Related]
10. Estimating the total genome length of a metagenomic sample using k-mers.
Hua K; Zhang X
BMC Genomics; 2019 Apr; 20(Suppl 2):183. PubMed ID: 30967110
[TBL] [Abstract][Full Text] [Related]
11. Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system.
Somerville V; Lutz S; Schmid M; Frei D; Moser A; Irmler S; Frey JE; Ahrens CH
BMC Microbiol; 2019 Jun; 19(1):143. PubMed ID: 31238873
[TBL] [Abstract][Full Text] [Related]
12. Selection of marker genes for genetic barcoding of microorganisms and binning of metagenomic reads by Barcoder software tools.
Rotimi AM; Pierneef R; Reva ON
BMC Bioinformatics; 2018 Aug; 19(1):309. PubMed ID: 30165813
[TBL] [Abstract][Full Text] [Related]
13. Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation.
Beaulaurier J; Zhu S; Deikus G; Mogno I; Zhang XS; Davis-Richardson A; Canepa R; Triplett EW; Faith JJ; Sebra R; Schadt EE; Fang G
Nat Biotechnol; 2018 Jan; 36(1):61-69. PubMed ID: 29227468
[TBL] [Abstract][Full Text] [Related]
14. Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences.
Wang Z; Wang Y; Fuhrman JA; Sun F; Zhu S
Brief Bioinform; 2020 May; 21(3):777-790. PubMed ID: 30860572
[TBL] [Abstract][Full Text] [Related]
15. Species classifier choice is a key consideration when analysing low-complexity food microbiome data.
Walsh AM; Crispie F; O'Sullivan O; Finnegan L; Claesson MJ; Cotter PD
Microbiome; 2018 Mar; 6(1):50. PubMed ID: 29554948
[TBL] [Abstract][Full Text] [Related]
16. METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks.
Zhou Z; Tran PQ; Breister AM; Liu Y; Kieft K; Cowley ES; Karaoz U; Anantharaman K
Microbiome; 2022 Feb; 10(1):33. PubMed ID: 35172890
[TBL] [Abstract][Full Text] [Related]
17. Improving the sensitivity of long read overlap detection using grouped short k-mer matches.
Du N; Chen J; Sun Y
BMC Genomics; 2019 Apr; 20(Suppl 2):190. PubMed ID: 30967123
[TBL] [Abstract][Full Text] [Related]
18. Strainberry: automated strain separation in low-complexity metagenomes using long reads.
Vicedomini R; Quince C; Darling AE; Chikhi R
Nat Commun; 2021 Jul; 12(1):4485. PubMed ID: 34301928
[TBL] [Abstract][Full Text] [Related]
19. Profiling microbial strains in urban environments using metagenomic sequencing data.
Zolfo M; Asnicar F; Manghi P; Pasolli E; Tett A; Segata N
Biol Direct; 2018 May; 13(1):9. PubMed ID: 29743119
[TBL] [Abstract][Full Text] [Related]
20. Improved metagenome binning and assembly using deep variational autoencoders.
Nissen JN; Johansen J; Allesøe RL; Sønderby CK; Armenteros JJA; Grønbech CH; Jensen LJ; Nielsen HB; Petersen TN; Winther O; Rasmussen S
Nat Biotechnol; 2021 May; 39(5):555-560. PubMed ID: 33398153
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
