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SqueezeMeta, a highly portable, fully automatic metagenomic analysis pipeline

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/0471250953.bi1108s33openalex-snapshot

Next Generation Sequence Assembly with AMOS

inferredcites →https://doi.org/10.1002/9781118010518.ch37openalex-snapshot

The Metagenomics RAST Server: A Public Resource for the Automatic Phylogenetic and Functional Analysis of Metagenomes

inferredcites →https://doi.org/10.1016/j.cub.2015.04.055openalex-snapshot

Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota

inferredcites →https://doi.org/10.1038/nature16996openalex-snapshot

Real-time, portable genome sequencing for Ebola surveillance

inferredcites →https://doi.org/10.1038/nbt.3423openalex-snapshot

Three decades of nanopore sequencing

inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot

Fast gapped-read alignment with Bowtie 2

inferredcites →https://doi.org/10.1038/nmeth.3176openalex-snapshot

Fast and sensitive protein alignment using DIAMOND

inferredcites →https://doi.org/10.1038/s41564-018-0171-1openalex-snapshot

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

inferredcites →https://doi.org/10.1038/sdata.2017.203openalex-snapshot

The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans

inferredcites →https://doi.org/10.1089/cmb.2012.0021openalex-snapshot

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

inferredcites →https://doi.org/10.1093/bioinformatics/btn355openalex-snapshot

Metagenomics reveals our incomplete knowledge of global diversity

inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot

BEDTools: a flexible suite of utilities for comparing genomic features

inferredcites →https://doi.org/10.1093/bioinformatics/btq536openalex-snapshot

SmashCommunity: a metagenomic annotation and analysis tool

inferredcites →https://doi.org/10.1093/bioinformatics/btr026openalex-snapshot

Quality control and preprocessing of metagenomic datasets

inferredcites →https://doi.org/10.1093/bioinformatics/bts565openalex-snapshot

CD-HIT: accelerated for clustering the next-generation sequencing data

inferredcites →https://doi.org/10.1093/bioinformatics/btu153openalex-snapshot

Prokka: rapid prokaryotic genome annotation

inferredcites →https://doi.org/10.1093/bioinformatics/btv033openalex-snapshot

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

inferredcites →https://doi.org/10.1093/bioinformatics/btv638openalex-snapshot

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

inferredcites →https://doi.org/10.1093/bioinformatics/bty191openalex-snapshot

Minimap2: pairwise alignment for nucleotide sequences

inferredcites →https://doi.org/10.1093/nar/27.1.29openalex-snapshot

KEGG: Kyoto Encyclopedia of Genes and Genomes

inferredcites →https://doi.org/10.1093/nar/28.1.27openalex-snapshot

KEGG: Kyoto Encyclopedia of Genes and Genomes

inferredcites →https://doi.org/10.1093/nar/gkt1223openalex-snapshot

Pfam: the protein families database

inferredcites →https://doi.org/10.1093/nar/gku169openalex-snapshot

MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences

inferredcites →https://doi.org/10.1093/nar/gkv1248openalex-snapshot

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

inferredcites →https://doi.org/10.1101/gr.186072.114openalex-snapshot

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

inferredcites →https://doi.org/10.1101/gr.215087.116openalex-snapshot

Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation

inferredcites →https://doi.org/10.1109/tcsvt.2017.2671899openalex-snapshot

LETRIST: Locally Encoded Transform Feature Histogram for Rotation-Invariant Texture Classification

inferredcites →https://doi.org/10.1128/aem.00062-07openalex-snapshot

Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy

inferredcites →https://doi.org/10.1128/aem.02181-07openalex-snapshot

Metagenomics: Read Length Matters

inferredcites →https://doi.org/10.1142/9781848165632_0019openalex-snapshot

A NEW GENERATION OF HOMOLOGY SEARCH TOOLS BASED ON PROBABILISTIC INFERENCE

inferredcites →https://doi.org/10.1186/1471-2105-10-359openalex-snapshot

Analysis and comparison of very large metagenomes with fast clustering and functional annotation

inferredcites →https://doi.org/10.1186/1471-2105-11-119openalex-snapshot

Prodigal: prokaryotic gene recognition and translation initiation site identification

inferredcites →https://doi.org/10.1186/1471-2105-8-64openalex-snapshot

Minimus: a fast, lightweight genome assembler

inferredcites →https://doi.org/10.1186/1471-2105-9-386openalex-snapshot

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

inferredcites →https://doi.org/10.1186/s12859-016-1278-0openalex-snapshot

FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies

inferredcites →https://doi.org/10.1186/s12859-018-2028-2openalex-snapshot

Spherical: an iterative workflow for assembling metagenomic datasets

inferredcites →https://doi.org/10.1186/s12859-018-2189-zopenalex-snapshot

SAMSA2: a standalone metatranscriptome analysis pipeline

inferredcites →https://doi.org/10.1186/s13059-015-0677-2openalex-snapshot

Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella

inferredcites →https://doi.org/10.1186/s13059-016-1116-8openalex-snapshot

IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses

inferredcites →https://doi.org/10.1186/s40168-018-0541-1openalex-snapshot

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

inferredcites →https://doi.org/10.1371/journal.pcbi.1000410openalex-snapshot

Understanding the Adaptive Growth Strategy of Lactobacillus plantarum by In Silico Optimisation

inferredcites →https://doi.org/10.1371/journal.pcbi.1000465openalex-snapshot

A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes

inferredcites →https://doi.org/10.1371/journal.pcbi.1002358openalex-snapshot

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

inferredcites →https://doi.org/10.1371/journal.pone.0105776openalex-snapshot

Comparative Analysis of Functional Metagenomic Annotation and the Mappability of Short Reads

inferredcites →https://doi.org/10.7171/jbt.17-2801-009openalex-snapshot

Real-Time DNA Sequencing in the Antarctic Dry Valleys Using the Oxford Nanopore Sequencer

inferredcites →https://doi.org/10.7717/peerj.1165openalex-snapshot

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

inferredcites →https://doi.org/10.7717/peerj.1223openalex-snapshot

Comparative genomics of non-pseudomonal bacterial species colonising paediatric cystic fibrosis patients

inferredcites →https://doi.org/10.7717/peerj.1319openalex-snapshot

Anvi’o: an advanced analysis and visualization platform for ‘omics data

inferredcites →https://doi.org/10.7717/peerj.520openalex-snapshot

Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/9783527844340.ch35openalex-snapshot

Bioinformatic‐driven Research in Microbial Enzymes: An Overview

inferred← citeshttps://doi.org/10.1016/j.egg.2023.100160openalex-snapshot

Taxonomic and functional metagenomics profiling of Tuwa and Unnai hot springs microbial communities

inferred← citeshttps://doi.org/10.1016/j.scitotenv.2019.135107openalex-snapshot

Rare bacteria in seawater are dominant in the bacterial assemblage associated with the Bloom-forming dinoflagellate Noctiluca scintillans

inferred← citeshttps://doi.org/10.1016/j.scitotenv.2019.135152openalex-snapshot

Taxonomic and functional diversity of the microbiome in a jet fuel contaminated site as revealed by combined application of in situ microcosms with metagenomic analysis

inferred← citeshttps://doi.org/10.1016/j.scitotenv.2021.149208openalex-snapshot

Distinct metabolic strategies of the dominant heterotrophic bacterial groups associated with marine Synechococcus

inferred← citeshttps://doi.org/10.1073/pnas.1808176115openalex-snapshot

Viable cyanobacteria in the deep continental subsurface

inferred← citeshttps://doi.org/10.1093/bioadv/vbaf152openalex-snapshot

BugBuster: a novel automatic and reproducible workflow for metagenomic data analysis

inferred← citeshttps://doi.org/10.1093/nargab/lqac007openalex-snapshot

nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning

inferred← citeshttps://doi.org/10.1111/1755-0998.13826openalex-snapshot

Exploring environmental intra‐species diversity through non‐redundant pangenome assemblies

inferred← citeshttps://doi.org/10.1111/1755-0998.13996openalex-snapshot

MOSCA 2.0: A bioinformatics framework for metagenomics, metatranscriptomics and metaproteomics data analysis and visualization

inferred← citeshttps://doi.org/10.1111/nph.19252openalex-snapshot

Simplification of soil biota communities impairs nutrient recycling and enhances above‐ and belowground nitrogen losses

inferred← citeshttps://doi.org/10.1111/nph.20118openalex-snapshot

Evolutionarily conserved core microbiota as an extended trait in nitrogen acquisition strategy of herbaceous species

inferred← citeshttps://doi.org/10.1163/18762891-bja00017openalex-snapshot

Gut microbiome composition and functionality impact the responsiveness to a dairy-based product containing galacto-oligosaccharides for improving sleep quality in adults

inferred← citeshttps://doi.org/10.1186/s12859-021-04038-2openalex-snapshot

ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data

inferred← citeshttps://doi.org/10.1186/s12864-019-6289-6openalex-snapshot

Assessing the performance of different approaches for functional and taxonomic annotation of metagenomes

inferred← citeshttps://doi.org/10.1186/s42523-021-00125-0openalex-snapshot

Characterisation of the rumen resistome in Spanish dairy cattle

inferred← citeshttps://doi.org/10.1590/1678-7757-2023-0214openalex-snapshot

Biofilm dysbiosis and caries activity: a surface or an individual issue?

inferred← citeshttps://doi.org/10.18805/bkap637openalex-snapshot

Metagenomics and Its Tools and Softwares

inferred← citeshttps://doi.org/10.26686/wgtn.24187935openalex-snapshot

New methods for the discovery of natural products from understudied and uncultivated bacterial phyla

inferred← citeshttps://doi.org/10.30829/contagion.v5i3.15393openalex-snapshot

Comparasion of Microbiome Composition in Acne Vulgaris Using Metagenomic Shotgun and 16s Rrna

inferred← citeshttps://doi.org/10.3389/fmicb.2018.03349openalex-snapshot

SqueezeMeta, A Highly Portable, Fully Automatic Metagenomic Analysis Pipeline

inferred← citeshttps://doi.org/10.3389/fmicb.2024.1481702openalex-snapshot

Specialized Bacteroidetes dominate the Arctic Ocean during marine spring blooms

inferred← citeshttps://doi.org/10.3390/fermentation11100568openalex-snapshot

Metatranscriptome Analysis of Sheep Rumen Reveals Methane Production Changes Induced by Moringa oleifera as a Dietary Supplement

inferred← citeshttps://doi.org/10.5194/bg-18-2091-2021openalex-snapshot

Metagenomic insights into the metabolism of microbial communities that mediate iron and methane cycling in Lake Kinneret iron-rich methanic sediments

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