Metagenomics binning of long reads using read-overlap graphs

DOI10.1007/978-3-031-06220-9_15MaRDI QIDQ2163969zbMATH OpenOpenAlexFDO

Authors Anuradha Wickramarachchi, Yu Lin

Publication date 11 August 2022

Full work available at URL https://doi.org/10.1007/978-3-031-06220-9_15

zbMATH Keywords

long readsmetagenomics binningread-overlap graph

Mathematics Subject Classification ID

Computational methods for problems pertaining to biology (92-08) Genetics and epigenetics (92D10)

Recommendations

• LRBinner: Binning Long Reads in Metagenomics Datasets
• Graphbin2: refined and overlapped binning of metagenomic contigs using assembly graphs
• MetaCoAG: binning metagenomic contigs via composition, coverage and assembly graphs
• Metagenomic reads binning with spaced seeds
• Long Reads Enable Accurate Estimates of Complexity of Metagenomes

Cites work

• scientific article; zbMATH DE number 2101406 (Why is no real title available?)
• LRBinner: Binning Long Reads in Metagenomics Datasets
• Silhouettes: a graphical aid to the interpretation and validation of cluster analysis

Cited in

(11)

• oblr
• Metagenomic reads binning with spaced seeds
• MetaCoAG: binning metagenomic contigs via composition, coverage and assembly graphs
• CLMB: deep contrastive learning for robust metagenomic binning
• Predicting the metagenomics content with multiple CART trees
• Long Reads Enable Accurate Estimates of Complexity of Metagenomes
• Accurate Reconstruction of Microbial Strains from Metagenomic Sequencing Using Representative Reference Genomes
• MAGE: strain level profiling of metagenome samples
• LRBinner: Binning Long Reads in Metagenomics Datasets
• Graphbin2: refined and overlapped binning of metagenomic contigs using assembly graphs
• Prokrustean graph: a substring index for rapid k-mer size analysis

Describes a project that uses

Uses Software

• PyTorch
• Silhouettes
• hdbscan
• OGRE
• MetaBAT
• MaxBin
• MetaBCC-LR
• LRBinner
• Seq2Vec
• AMBER
• MetaQUAST
• Centrifuge
• RAPIDS
• UMAP
• metaFlye
• SimLoRD
• Minimap2
• GitHub

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