ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data

Kieser, Silas; Brown, Joseph; Zdobnov, Evgeny M.; Trajkovski, Mirko; McCue, Lee Ann

doi:10.1186/s12859-020-03585-4

Cited by 132 publications

(138 citation statements)

References 42 publications

Supporting

Mentioning

125

Contrasting

Order By: Relevance

“…Chloroheliales' (Supplementary Note 1). The single enrichment culture metagenome was processed using ATLAS version 2.2.0 52,55 for read quality control, assembly and genome binning. A single genome bin was classified using the GTDB-Tk 21 to the Chloroflexota phylum.…”

Section: Genome Assembly and Binningmentioning

confidence: 99%

Anoxygenic phototrophicChloroflexotamember uses a Type I reaction center

Tsuji

Shaw

Nagashima

et al. 2020

Preprint

View full text Add to dashboard Cite

SummaryChlorophyll-based phototrophy is performed using quinone and/or Fe-S type reaction centers1,2. Unlike oxygenic phototrophs, where both reaction center classes are used in tandem as Photosystem II and Photosystem I, anoxygenic phototrophs use only one class of reaction center, termed Type II (RCII) or Type I (RCI) reaction centers, separately for phototrophy3. Here we report the cultivation and characterization of a filamentous anoxygenic phototroph within the Chloroflexota (formerly Chloroflexi4) phylum, provisionally named ‘Candidatus Chlorohelix allophototropha’, that performs phototrophy using a distinct fourth clade of RCI protein, despite placing sister taxonomically to RCII-utilizing Chloroflexota members. ‘Ca. Chx. allophototropha’ contains chlorosomes, uses bacteriochlorophyll c, and encodes the FMO protein like other RCI-utilizing phototrophs in the Chlorobiales and Chloracidobacterales orders5. ‘Ca. Chx. allophototropha’ also encodes the potential for carbon fixation using the Calvin-Benson-Bassham (CBB) cycle, unlike all known RCI-utilizing phototrophs6. The discovery of ‘Ca. Chx. allophototropha’, as the first representative of a novel Chloroflexota order (i.e., ‘Ca. Chloroheliales’), sheds light on longstanding questions about the evolution of photosynthesis, including the origin of chlorosomes among RCII-utilizing Chloroflexota members5,7. The Chloroflexota is now the only phylum outside the Cyanobacteria containing genomic potential for both quinone and Fe-S type reaction centers and can thus serve as an additional system for exploring fundamental questions about the evolution of photosynthesis.

show abstract

Section: Genome Assembly and Binningmentioning

confidence: 99%

Anoxygenic phototrophicChloroflexotamember uses a Type I reaction center

Tsuji

Shaw

Nagashima

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…Quality assessment for completeness and contamination of sequence bins was performed using CheckM V1.0.18 software (33). Annotation of gene content was performed using the pipeline ATLAS-metagenome (34), which involves the prediction of open reading frames (ORFs) using Prodigal (35). Translated gene products were clustered using linclust (36) to generate non-redundant gene and protein catalogues, which were mapped to the eggNOG catalogue (37) using DIAMOND (38).…”

Section: Data Preprocessing Assembly Binning and Annotationsmentioning

confidence: 99%

Unpicking the mysterious symbiosis ofMycoplasmain salmonids

Cheaib

Yang

Kazlauskaite

et al. 2020

Preprint

View full text Add to dashboard Cite

Lacking a peptidoglycan cell wall, mycoplasmas are the smallest self-replicating life forms. Members of this bacterial genus are known to parasitise a wide array of metazoans including vertebrates. Whilst much research has been significant targeted at parasitic mammalian mycoplasmas, very little is known about their role in other vertebrates. In the current study, we aim to explore the biology and evolution of Mycoplasma in salmonids, including cellular niche, genome size structure and gene content. Using Fluorescence in-situ hybridisation (FISH), mycoplasmas were identified in epithelial tissues across the digestive tract (stomach, pyloric caecum and midgut) during the developmental stages (eggs, parr, subadult) of farmed Atlantic salmon (Salmo salar), showing a high abundance in acidic compartments. With high throughput sequencing from subadults farmed Atlantic salmon, we assembled a nearly complete genome (~0.53 MB) via shotgun-metagenomics. The phylogenetic inference from the recovered genome revealed successful taxonomic proximity to Mycoplasma penetrans (~1.36 Mb) from the recovered genome. Although no significant correlation between genome size and its phylogeny was observed, we recovered functional signatures, especially, riboflavin encoding genes pathway and sugars transporters, suggesting a symbiotic relationship between Mycoplasma and the host. Though 247 strains of Mycoplasma are available in public databases, to the best of our knowledge, this is the first study to demonstrate an ecological and functional association between Mycoplasma and Salmo salar which delineates symbiotic reductive evolution and genome erosion primarily and also serves as a proxy for salmonid health in aquaculture processes (cell lines, in vitro gut models).

show abstract

“…Several workflows for metagenomic analyses have been published, including MetaWRAP(v1.2.1) [ 15 ], Anvi’o [ 16 ], SAMSA2 [ 17 ], Humann [ 18 ], MG-Rast [ 19 ], ATLAS [ 20 ], or Sunbeam [ 21 ]. Unlike those, MUFFIN allows for a hybrid metagenomic approach combining the strengths of short and long reads.…”

Section: Introductionmentioning

confidence: 99%

Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN)

et al. 2021

View full text Add to dashboard Cite

Metagenomics has redefined many areas of microbiology. However, metagenome-assembled genomes (MAGs) are often fragmented, primarily when sequencing was performed with short reads. Recent long-read sequencing technologies promise to improve genome reconstruction. However, the integration of two different sequencing modalities makes downstream analyses complex. We, therefore, developed MUFFIN, a complete metagenomic workflow that uses short and long reads to produce high-quality bins and their annotations. The workflow is written by using Nextflow, a workflow orchestration software, to achieve high reproducibility and fast and straightforward use. This workflow also produces the taxonomic classification and KEGG pathways of the bins and can be further used for quantification and annotation by providing RNA-Seq data (optionally). We tested the workflow using twenty biogas reactor samples and assessed the capacity of MUFFIN to process and output relevant files needed to analyze the microbial community and their function. MUFFIN produces functional pathway predictions and, if provided de novo metatranscript annotations across the metagenomic sample and for each bin. MUFFIN is available on github under GNUv3 licence: https://github.com/RVanDamme/MUFFIN.

show abstract

ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data

Cited by 132 publications

References 42 publications

Anoxygenic phototrophicChloroflexotamember uses a Type I reaction center

Anoxygenic phototrophicChloroflexotamember uses a Type I reaction center

Unpicking the mysterious symbiosis ofMycoplasmain salmonids

Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN)

Contact Info

Product

Resources

About