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Integrative workflows for metagenomic analysis
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instance of
scholarly article
1 reference
stated in
PubMed
review article
1 reference
stated in
Europe PubMed Central
title
Integrative workflows for metagenomic analysis
(English)
1 reference
stated in
PubMed
main subject
workflow
1 reference
based on heuristic
inferred from title
metagenomics
1 reference
based on heuristic
inferred from title
author name string
Efthymios Ladoukakis
series ordinal
1
1 reference
stated in
Crossref
Fragiskos N. Kolisis
series ordinal
2
1 reference
stated in
Crossref
Aristotelis A. Chatziioannou
series ordinal
3
1 reference
stated in
Crossref
language of work or name
English
1 reference
stated in
PubMed
publication date
2014
1 reference
stated in
PubMed
published in
Frontiers in Cell and Developmental Biology
1 reference
stated in
Crossref
volume
2
1 reference
stated in
PubMed
page(s)
70
1 reference
stated in
PubMed
cites work
Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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21 March 2017
HMMER web server: interactive sequence similarity searching
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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21 March 2017
SmashCommunity: a metagenomic annotation and analysis tool
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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21 March 2017
Ab initio gene identification in metagenomic sequences
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stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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21 March 2017
QIIME allows analysis of high-throughput community sequencing data
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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21 March 2017
The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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21 March 2017
Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities
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PubMed Central
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21 March 2017
The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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21 March 2017
Velvet: algorithms for de novo short read assembly using de Bruijn graphs
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PubMed Central
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21 March 2017
The RAST Server: rapid annotations using subsystems technology
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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21 March 2017
CAMERA: a community resource for metagenomics
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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21 March 2017
MEGAN analysis of metagenomic data
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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21 March 2017
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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21 March 2017
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
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PubMed Central
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21 March 2017
UniProt: the Universal Protein knowledgebase
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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21 March 2017
Enzyme-specific profiles for genome annotation: PRIAM
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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21 March 2017
The Uncultured Microbial Majority
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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21 March 2017
The Bioperl toolkit: Perl modules for the life sciences
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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21 March 2017
BLAT—The BLAST-Like Alignment Tool
2 references
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
retrieved
21 March 2017
stated in
Crossref
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https://api.crossref.org/works/10.3389%2FFCELL.2014.00070
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22 April 2017
Basic local alignment search tool
2 references
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
retrieved
21 March 2017
stated in
Crossref
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https://api.crossref.org/works/10.3389%2FFCELL.2014.00070
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22 April 2017
16S ribosomal DNA amplification for phylogenetic study
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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21 March 2017
DNA sequencing with chain-terminating inhibitors
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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21 March 2017
The case for cloud computing in genome informatics
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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21 March 2017
Fast gapped-read alignment with Bowtie 2
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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21 March 2017
Sequencing technologies - the next generation
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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21 March 2017
The COG database: a tool for genome-scale analysis of protein functions and evolution
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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21 March 2017
Next-generation DNA sequencing methods
2 references
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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21 March 2017
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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7 April 2017
Pfam: the protein families database
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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21 March 2017
PhymmBL expanded: confidence scores, custom databases, parallelization and more
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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21 March 2017
Search and clustering orders of magnitude faster than BLAST
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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7 April 2017
Next-generation DNA sequencing
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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7 April 2017
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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7 April 2017
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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7 April 2017
Galaxy: a platform for interactive large-scale genome analysis
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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7 April 2017
CD-HIT: accelerated for clustering the next-generation sequencing data
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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7 April 2017
Quality control and preprocessing of metagenomic datasets
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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7 April 2017
A whole-genome assembly of Drosophila
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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7 April 2017
eggNOG v4.0: nested orthology inference across 3686 organisms
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22 April 2017
MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences
1 reference
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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28 September 2017
MetaCluster-TA: taxonomic annotation for metagenomic data based on assembly-assisted binning
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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28 September 2017
SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads.
1 reference
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28 September 2017
IMG/M 4 version of the integrated metagenome comparative analysis system
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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28 September 2017
Kraken: a set of tools for quality control and analysis of high-throughput sequence data
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28 September 2017
HTQC: a fast quality control toolkit for Illumina sequencing data
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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28 September 2017
Protein data bank.
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28 September 2017
MetAMOS: a modular and open source metagenomic assembly and analysis pipeline
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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28 September 2017
Taxonomic binning of metagenome samples generated by next-generation sequencing technologies
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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28 September 2017
NGS QC Toolkit: a toolkit for quality control of next generation sequencing data
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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28 September 2017
ClaMS: A Classifier for Metagenomic Sequences
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
retrieved
28 September 2017
Interactive metagenomic visualization in a Web browser
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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28 September 2017
Bambus 2: scaffolding metagenomes
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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28 September 2017
CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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28 September 2017
Classifying short genomic fragments from novel lineages using composition and homology.
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
retrieved
28 September 2017
Meta-IDBA: a de Novo assembler for metagenomic data
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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28 September 2017
Next generation sequence assembly with AMOS.
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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28 September 2017
Benchmarking of gene prediction programs for metagenomic data
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
retrieved
28 September 2017
SPHINX--an algorithm for taxonomic binning of metagenomic sequences.
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
retrieved
28 September 2017
SmashCell: a software framework for the analysis of single-cell amplified genome sequences
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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28 September 2017
SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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28 September 2017
FragGeneScan: predicting genes in short and error-prone reads
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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28 September 2017
Cloud computing and the DNA data race
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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28 September 2017
Assembly algorithms for next-generation sequencing data
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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28 September 2017
Analysis and comparison of very large metagenomes with fast clustering and functional annotation
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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28 September 2017
Windshield splatter analysis with the Galaxy metagenomic pipeline
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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28 September 2017
FIGfams: yet another set of protein families
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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28 September 2017
Managing and analyzing next-generation sequence data
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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28 September 2017
Statistical methods for detecting differentially abundant features in clinical metagenomic samples
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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28 September 2017
Sequence assembly.
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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28 September 2017
MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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28 September 2017
Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories.
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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28 September 2017
IMG/M: a data management and analysis system for metagenomes
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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28 September 2017
EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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28 September 2017
ACLAME: a CLAssification of Mobile genetic Elements
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
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28 September 2017
The European database on small subunit ribosomal RNA.
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28 September 2017
The RDP-II (Ribosomal Database Project).
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28 September 2017
TIGRFAMs: a protein family resource for the functional identification of proteins
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PubMed Central
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28 September 2017
Phylogenetic analysis using PHYLIP.
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PubMed Central
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28 September 2017
Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products
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28 September 2017
PhyloSift: phylogenetic analysis of genomes and metagenomes
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31 May 2018
Orphelia: predicting genes in metagenomic sequencing reads
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
retrieved
31 May 2018
Sequencing errors and molecular evolutionary analysis
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237130
retrieved
31 May 2018
Comparison of statistical methods to classify environmental genomic fragments.
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.3389%2FFCELL.2014.00070
retrieved
21 January 2018
Microbiology. Genomes from metagenomics.
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.3389%2FFCELL.2014.00070
retrieved
21 January 2018
A novel heuristic for local multiple alignment of interspersed DNA repeats
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.3389%2FFCELL.2014.00070
retrieved
21 January 2018
GenBank
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.3389%2FFCELL.2014.00070
retrieved
21 January 2018
A System for Automated Bacterial (genome) Integrated Annotation--SABIA
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/25478562
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Identifiers
DOI
10.3389/FCELL.2014.00070
1 reference
stated in
Fatcat
reference URL
https://api.fatcat.wiki/v0/release/prevz6dl45adpjyvgacwt6ci2y
retrieved
30 July 2022
based on heuristic
mapped directly with Wikidata item
Fatcat ID
release_prevz6dl45adpjyvgacwt6ci2y
1 reference
stated in
Fatcat
reference URL
https://api.fatcat.wiki/v0/release/prevz6dl45adpjyvgacwt6ci2y
retrieved
30 July 2022
based on heuristic
mapped directly with Wikidata item
OpenCitations bibliographic resource ID
564927
1 reference
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
564927
PMC publication ID
4237130
1 reference
stated in
Fatcat
reference URL
https://api.fatcat.wiki/v0/release/prevz6dl45adpjyvgacwt6ci2y
retrieved
30 July 2022
based on heuristic
mapped directly with Wikidata item
PubMed publication ID
25478562
1 reference
stated in
Fatcat
reference URL
https://api.fatcat.wiki/v0/release/prevz6dl45adpjyvgacwt6ci2y
retrieved
30 July 2022
based on heuristic
mapped directly with Wikidata item
ResearchGate publication ID
269186409
0 references
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