4.6 Article

MetaGT: A pipeline for de novo assembly of metatranscriptomes with the aid of metagenomic data

Related references

Note: Only part of the references are listed.
Article Microbiology

Metagenomic and metatranscriptomic analyses reveal minor-yet-crucial roles of gut microbiome in deep-sea hydrothermal vent snail

Yi Yang et al.

Summary: The gut microbiome of the provannid snail Alviniconcha marisindica plays key nutritional and metabolic roles, contributing to the understanding of how deep-sea chemosymbiotic animals utilize available resources. The composition and abundance of the gut microbiota in A. marisindica differ from those of snails that do not rely on endosymbiosis. The gut microbiome assists in the use of inorganic compounds, digestion of host-ingested organics, and recycling of host metabolic waste, indicating the importance of gut microbial ecology for the survival of invertebrate hosts in extreme environments.

ANIMAL MICROBIOME (2022)

Article Biotechnology & Applied Microbiology

Improved metagenome binning and assembly using deep variational autoencoders

Jakob Nybo Nissen et al.

Summary: Despite recent advances in metagenomic binning, reconstruction of microbial species from metagenomics data remains challenging. Here we develop variational autoencoders for metagenomic binning (VAMB), a program that outperforms existing state-of-the-art binners in reconstructing near-complete genomes on simulated and real data. VAMB is able to separate closely related strains with high accuracy and showcase different geographical distribution patterns of human gut microbiome species.

NATURE BIOTECHNOLOGY (2021)

Article Biochemical Research Methods

Simulating Illumina metagenomic data with InSilicoSeq

Hadrien Gourle et al.

BIOINFORMATICS (2019)

Article Multidisciplinary Sciences

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

Jason Lloyd-Price et al.

NATURE (2019)

Article Biochemical Research Methods

Minimap2: pairwise alignment for nucleotide sequences

Heng Li

BIOINFORMATICS (2018)

Software Review Microbiology

MetaWRAP-a flexible pipeline for genome-resolved metagenomic data analysis

Gherman V. Uritskiy et al.

MICROBIOME (2018)

Article Biochemistry & Molecular Biology

metaSPAdes: a new versatile metagenomic assembler

Sergey Nurk et al.

GENOME RESEARCH (2017)

Letter Biotechnology & Applied Microbiology

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

Martin Steinegger et al.

NATURE BIOTECHNOLOGY (2017)

Article Biochemical Research Methods

Salmon provides fast and bias-aware quantification of transcript expression

Rob Patro et al.

NATURE METHODS (2017)

Article Biochemical Research Methods

Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis

Yuzhen Ye et al.

BIOINFORMATICS (2016)

Article Biochemical Research Methods

rnaQUAST: a quality assessment tool for de novo transcriptome assemblies

Elena Bushmanova et al.

BIOINFORMATICS (2016)

Article Biotechnology & Applied Microbiology

Near-optimal probabilistic RNA-seq quantification

Nicolas L. Bray et al.

NATURE BIOTECHNOLOGY (2016)

Article Biochemical Research Methods

IDBA-MTP: A Hybrid Metatranscriptomic Assembler Based on Protein Information

Henry C. M. Leung et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2015)

Article Biochemical Research Methods

Prokka: rapid prokaryotic genome annotation

Torsten Seemann

BIOINFORMATICS (2014)

Article Biochemical Research Methods

QUAST: quality assessment tool for genome assemblies

Alexey Gurevich et al.

BIOINFORMATICS (2013)

Article Biochemical Research Methods

IDBA-MT: De Novo Assembler for Metatranscriptomic Data Generated from Next-Generation Sequencing Technology

Henry C. M. Leung et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2013)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Multidisciplinary Sciences

Enterotypes of the human gut microbiome

Manimozhiyan Arumugam et al.

NATURE (2011)

Article Biochemical Research Methods

Prodigal: prokaryotic gene recognition and translation initiation site identification

Doug Hyatt et al.

BMC BIOINFORMATICS (2010)

Letter Biochemical Research Methods

QIIME allows analysis of high-throughput community sequencing data

J. Gregory Caporaso et al.

NATURE METHODS (2010)

Article Multidisciplinary Sciences

The Human Microbiome Project

Peter J. Turnbaugh et al.

NATURE (2007)

Article Biotechnology & Applied Microbiology

Analysis of microbial gene transcripts in environmental samples

RS Poretsky et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2005)