These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
2. HiFine: integrating Hi-C-based and shotgun-based methods to refine binning of metagenomic contigs. Du Y; Sun F Bioinformatics; 2022 May; 38(11):2973-2979. PubMed ID: 35482530 [TBL] [Abstract][Full Text] [Related]
3. MSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun metagenomic data. Plaza Oñate F; Le Chatelier E; Almeida M; Cervino ACL; Gauthier F; Magoulès F; Ehrlich SD; Pichaud M Bioinformatics; 2019 May; 35(9):1544-1552. PubMed ID: 30252023 [TBL] [Abstract][Full Text] [Related]
4. Metaviral SPAdes: assembly of viruses from metagenomic data. Antipov D; Raiko M; Lapidus A; Pevzner PA Bioinformatics; 2020 Aug; 36(14):4126-4129. PubMed ID: 32413137 [TBL] [Abstract][Full Text] [Related]
5. TIPP2: metagenomic taxonomic profiling using phylogenetic markers. Shah N; Molloy EK; Pop M; Warnow T Bioinformatics; 2021 Jul; 37(13):1839-1845. PubMed ID: 33471121 [TBL] [Abstract][Full Text] [Related]
6. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nielsen HB; Almeida M; Juncker AS; Rasmussen S; Li J; Sunagawa S; Plichta DR; Gautier L; Pedersen AG; Le Chatelier E; Pelletier E; Bonde I; Nielsen T; Manichanh C; Arumugam M; Batto JM; Quintanilha Dos Santos MB; Blom N; Borruel N; Burgdorf KS; Boumezbeur F; Casellas F; Doré J; Dworzynski P; Guarner F; Hansen T; Hildebrand F; Kaas RS; Kennedy S; Kristiansen K; Kultima JR; Léonard P; Levenez F; Lund O; Moumen B; Le Paslier D; Pons N; Pedersen O; Prifti E; Qin J; Raes J; Sørensen S; Tap J; Tims S; Ussery DW; Yamada T; ; Renault P; Sicheritz-Ponten T; Bork P; Wang J; Brunak S; Ehrlich SD; Nat Biotechnol; 2014 Aug; 32(8):822-8. PubMed ID: 24997787 [TBL] [Abstract][Full Text] [Related]
7. Improving contig binning of metagenomic data using [Formula: see text] oligonucleotide frequency dissimilarity. Wang Y; Wang K; Lu YY; Sun F BMC Bioinformatics; 2017 Sep; 18(1):425. PubMed ID: 28931373 [TBL] [Abstract][Full Text] [Related]
8. CoCoNet: an efficient deep learning tool for viral metagenome binning. Arisdakessian CG; Nigro OD; Steward GF; Poisson G; Belcaid M Bioinformatics; 2021 Sep; 37(18):2803-2810. PubMed ID: 33822891 [TBL] [Abstract][Full Text] [Related]
9. Metagenomic binning with assembly graph embeddings. Lamurias A; Sereika M; Albertsen M; Hose K; Nielsen TD Bioinformatics; 2022 Sep; 38(19):4481-4487. PubMed ID: 35972375 [TBL] [Abstract][Full Text] [Related]
10. GraphBin: refined binning of metagenomic contigs using assembly graphs. Mallawaarachchi V; Wickramarachchi A; Lin Y Bioinformatics; 2020 Jun; 36(11):3307-3313. PubMed ID: 32167528 [TBL] [Abstract][Full Text] [Related]
15. MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. Wu YW; Tang YH; Tringe SG; Simmons BA; Singer SW Microbiome; 2014; 2():26. PubMed ID: 25136443 [TBL] [Abstract][Full Text] [Related]
16. 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]
17. MetaID: a novel method for identification and quantification of metagenomic samples. Srinivasan SM; Guda C BMC Genomics; 2013; 14 Suppl 8(Suppl 8):S4. PubMed ID: 24564518 [TBL] [Abstract][Full Text] [Related]
18. Capturing variation in metagenomic assembly graphs with MetaCortex. Martin S; Ayling M; Patrono L; Caccamo M; Murcia P; Leggett RM Bioinformatics; 2023 Jan; 39(1):. PubMed ID: 36722204 [TBL] [Abstract][Full Text] [Related]
19. Folic acid supplementation and malaria susceptibility and severity among people taking antifolate antimalarial drugs in endemic areas. Crider K; Williams J; Qi YP; Gutman J; Yeung L; Mai C; Finkelstain J; Mehta S; Pons-Duran C; Menéndez C; Moraleda C; Rogers L; Daniels K; Green P Cochrane Database Syst Rev; 2022 Feb; 2(2022):. PubMed ID: 36321557 [TBL] [Abstract][Full Text] [Related]
20. A robust and accurate binning algorithm for metagenomic sequences with arbitrary species abundance ratio. Leung HC; Yiu SM; Yang B; Peng Y; Wang Y; Liu Z; Chen J; Qin J; Li R; Chin FY Bioinformatics; 2011 Jun; 27(11):1489-95. PubMed ID: 21493653 [TBL] [Abstract][Full Text] [Related] [Next] [New Search]