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NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language

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What this work says

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

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Effectiveness and efficiency of a domain-specific language for high-performance marine ecosystem simulation: a controlled experiment

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The Human Gut Microbiome: From Association to Modulation

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An integrated catalog of reference genes in the human gut microbiome

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A catalog of the mouse gut metagenome

inferredcites →https://doi.org/10.1038/nbt.3820openalex-snapshot

Nextflow enables reproducible computational workflows

inferredcites →https://doi.org/10.1038/nm.4517openalex-snapshot

Current understanding of the human microbiome

inferredcites →https://doi.org/10.1038/nmeth.2575openalex-snapshot

Accurate and universal delineation of prokaryotic species

inferredcites →https://doi.org/10.1038/nmeth.2693openalex-snapshot

Metagenomic species profiling using universal phylogenetic marker genes

inferredcites →https://doi.org/10.1038/nmeth.3589openalex-snapshot

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

inferredcites →https://doi.org/10.1038/nmeth.4197openalex-snapshot

Salmon provides fast and bias-aware quantification of transcript expression

inferredcites →https://doi.org/10.1038/nmeth.4458openalex-snapshot

Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

inferredcites →https://doi.org/10.1038/nmicrobiol.2016.161openalex-snapshot

A reference gene catalogue of the pig gut microbiome

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Bioconda: sustainable and comprehensive software distribution for the life sciences

inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot

The Sequence Alignment/Map format and SAMtools

inferredcites →https://doi.org/10.1093/bioinformatics/bts480openalex-snapshot

Snakemake—a scalable bioinformatics workflow engine

inferredcites →https://doi.org/10.1093/bioinformatics/btu638openalex-snapshot

HTSeq—a Python framework to work with high-throughput sequencing data

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/btw183openalex-snapshot

MOCAT2: a metagenomic assembly, annotation and profiling framework

inferredcites →https://doi.org/10.1093/bioinformatics/btx192openalex-snapshot

BioContainers: an open-source and community-driven framework for software standardization

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

Minimap2: pairwise alignment for nucleotide sequences

inferredcites →https://doi.org/10.1093/molbev/msx148openalex-snapshot

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

inferredcites →https://doi.org/10.1093/nar/gki866openalex-snapshot

The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes

inferredcites →https://doi.org/10.1093/nar/gkt1076openalex-snapshot

Data, information, knowledge and principle: back to metabolism in KEGG

inferredcites →https://doi.org/10.1093/nar/gkv1049openalex-snapshot

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

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/10.1101/155358openalex-snapshot

Evaluating Metagenome Assembly on a Simple Defined Community with Many Strain Variants

inferredcites →https://doi.org/10.1109/5992.881708openalex-snapshot

Making scientific computations reproducible

inferredcites →https://doi.org/10.1109/mcse.2009.15openalex-snapshot

Reproducible Research in Computational Harmonic Analysis

inferredcites →https://doi.org/10.1109/mcse.2014.94openalex-snapshot

Reproducible Research as a Community Effort: Lessons from the Madagascar Project

inferredcites →https://doi.org/10.1109/mcse.2018.108162940openalex-snapshot

Software Engineering for Computational Science: Past, Present, Future

inferredcites →https://doi.org/10.1109/msp.2009.932122openalex-snapshot

Reproducible research in signal processing

inferredcites →https://doi.org/10.1126/science.1171700openalex-snapshot

Topographical and Temporal Diversity of the Human Skin Microbiome

inferredcites →https://doi.org/10.1126/science.1261359openalex-snapshot

Structure and function of the global ocean microbiome

inferredcites →https://doi.org/10.1145/2063348.2063374openalex-snapshot

A survey of the practice of computational science

inferredcites →https://doi.org/10.1186/1471-2105-11-1openalex-snapshot

Detection of gene pathways with predictive power for breast cancer prognosis

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/gb-2011-12-6-r60openalex-snapshot

Metagenomic biomarker discovery and explanation

inferredcites →https://doi.org/10.1186/gb-2013-14-1-r2openalex-snapshot

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

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/s40168-018-0450-3openalex-snapshot

Similarity of the dog and human gut microbiomes in gene content and response to diet

inferredcites →https://doi.org/10.1371/journal.pbio.1001745openalex-snapshot

Best Practices for Scientific Computing

inferredcites →https://doi.org/10.1371/journal.pone.0047656openalex-snapshot

MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit

inferredcites →https://doi.org/10.1371/journal.pone.0061217openalex-snapshot

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

inferredcites →https://doi.org/10.15252/msb.20145645openalex-snapshot

Potential of fecal microbiota for early‐stage detection of colorectal cancer

inferredcites →https://doi.org/10.5334/jors.161openalex-snapshot

Jug: Software for Parallel Reproducible Computation in Python

inferredcites →https://doi.org/10.6084/m9.figshare.3115156openalex-snapshot

Common Workflow Language, draft 3

inferredcites →https://doi.org/10.6084/m9.figshare.963153.v1openalex-snapshot

Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM

inferredcites →https://doi.org/10.7717/peerj-cs.86openalex-snapshot

Software citation principles

What points at this work

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

inferred← citeshttps://doi.org/10.1038/s41586-021-04177-9openalex-snapshot

Combinatorial, additive and dose-dependent drug–microbiome associations

inferred← citeshttps://doi.org/10.1038/s41586-021-04233-4openalex-snapshot

Towards the biogeography of prokaryotic genes

inferred← citeshttps://doi.org/10.1038/s41591-022-01913-0openalex-snapshot

Drivers and determinants of strain dynamics following fecal microbiota transplantation

inferred← citeshttps://doi.org/10.1038/s41596-024-00999-9openalex-snapshot

Identification and validation of microbial biomarkers from cross-cohort datasets using xMarkerFinder

inferred← citeshttps://doi.org/10.2139/ssrn.5040703openalex-snapshot

Gut Microbiome and Metabolite Alterations in Atrial Fibrillation

inferred← citeshttps://doi.org/10.70675/88df14a5z15aaz45aezac37z2a096f79eef8openalex-snapshot

Reconstitution de pan-génomes microbiens par séquençage métagénomique aléatoire : Application à l’étude du microbiote intestinal humain

inferred← citeshttps://doi.org/10.70675/c82d5d0ez084dz4ae6za044zfede1667bb46openalex-snapshot

Analyse de l'impact de Parvimonas micra sur les cellules coliques de l'hôte

inferred← citeshttps://doi.org/10.7554/elife.42693openalex-snapshot

Extensive transmission of microbes along the gastrointestinal tract

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