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SqueezeMeta, A Highly Portable, Fully Automatic Metagenomic Analysis Pipeline
46/46 checkable references clean · checked 2026-07-23
Every reference with a DOI in the deposited reference list resolved to a known work in Crossref or DataCite at the dated check, and none carried a retraction, withdrawal, or removal notice.
The 46 checked references that resolve
resolves10.1371/journal.pcbi.1002358
Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome
resolves10.1089/cmb.2012.0021
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
resolves10.1371/journal.pone.0105776
Comparative Analysis of Functional Metagenomic Annotation and the Mappability of Short Reads
resolves10.1142/9781848165632_0019
A NEW GENERATION OF HOMOLOGY SEARCH TOOLS BASED ON PROBABILISTIC INFERENCE
resolves10.1093/bioinformatics/bts565
CD-HIT: accelerated for clustering the next-generation sequencing data
resolves10.1002/9781118010518.ch37
The Metagenomics RAST Server: A Public Resource for the Automatic Phylogenetic and Functional Analysis of Metagenomes
resolves10.1186/s12859-018-2028-2
Spherical: an iterative workflow for assembling metagenomic datasets
resolves10.1093/nar/gkv1248
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences
resolves10.1186/1471-2105-11-119
Prodigal: prokaryotic gene recognition and translation initiation site identification
resolves10.7171/jbt.17-2801-009
Real-Time DNA Sequencing in the Antarctic Dry Valleys Using the Oxford Nanopore Sequencer
resolves10.7717/peerj.1165
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
resolves10.1186/s12859-016-1278-0
FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies
resolves10.1101/gr.215087.116
Canu: scalable and accurate long-read assembly via adaptive
<i>k</i>
-mer weighting and repeat separation
resolves10.1093/bioinformatics/btv033
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct <i>de Bruijn</i> graph
resolves10.1186/1471-2105-10-359
Analysis and comparison of very large metagenomes with fast clustering and functional annotation
resolves10.7717/peerj.520
Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition
resolves10.1093/nar/gku169
MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences
resolves10.1186/1471-2105-9-386
The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes
resolves10.1186/s13059-016-1116-8
IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses
resolves10.1101/gr.186072.114
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
resolves10.1093/bioinformatics/btn355
Metagenomics reveals our incomplete knowledge of global diversity
resolves10.1186/s13059-015-0677-2
Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella
resolves10.1093/bioinformatics/btq033
BEDTools: a flexible suite of utilities for comparing genomic features
resolves10.1038/s41564-018-0171-1
Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy
resolves10.1038/sdata.2017.203
The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans
resolves10.1186/s40168-018-0541-1
MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis
resolves10.1128/AEM.00062-07
Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
resolves10.1093/bioinformatics/btv638
MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets
resolves10.1371/journal.pcbi.1000465
A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes
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