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View article: Critical Assessment of Metagenome Interpretation: the second round of challenges
Critical Assessment of Metagenome Interpretation: the second round of challenges Open
Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on r…
View article: Haploflow: strain-resolved de novo assembly of viral genomes
Haploflow: strain-resolved de novo assembly of viral genomes Open
With viral infections, multiple related viral strains are often present due to coinfection or within-host evolution. We describe Haploflow, a deBruijn graph-based assembler for de novo genome assembly of viral strains from mixed sequence s…
View article: Critical Assessment of Metagenome Interpretation - the second round of challenges
Critical Assessment of Metagenome Interpretation - the second round of challenges Open
Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the community-driven initiative for the Critical Assessment of Metagenome Interpretation (CAMI). In its second challenge, CAMI engaged the communi…
View article: Assemblies of the CAMI 2 challenge data sets
Assemblies of the CAMI 2 challenge data sets Open
Assembly submissions, including participants' submissions, of the CAMI 2 challenge data sets. The gold standards can be found either on the CAMI 2 challenge website: https://data.cami-challenge.org/participate or in publisso alongside the …
View article: Assemblies of the CAMI 2 challenge data sets
Assemblies of the CAMI 2 challenge data sets Open
Assembly submissions, including participants' submissions, of the CAMI 2 challenge data sets. The gold standards can be found either on the CAMI 2 challenge website: https://data.cami-challenge.org/participate or in publisso alongside the …
View article: Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit
Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit Open
View article: Haploflow: Strain-resolved<i>de novo</i>assembly of viral genomes
Haploflow: Strain-resolved<i>de novo</i>assembly of viral genomes Open
In viral infections often multiple related viral strains are present, due to coinfection or within-host evolution. We describe Haploflow, a de Bruijn graph-based assembler for de novo genome assembly of viral strains from mixed sequence sa…
View article: Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research
Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research Open
SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causes the infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformat…
View article: Tutorial: Assessing metagenomics software with the CAMI benchmarking toolkit
Tutorial: Assessing metagenomics software with the CAMI benchmarking toolkit Open
Computational methods are key in microbiome research, and obtaining a quantitative and unbiased performance estimate is important for method developers and applied researchers. For meaningful comparisons between methods, to identify best p…
View article: Evaluating assembly and variant calling software for strain-resolved analysis of large DNA viruses
Evaluating assembly and variant calling software for strain-resolved analysis of large DNA viruses Open
Infection with human cytomegalovirus (HCMV) can cause severe complications in immunocompromised individuals and congenitally infected children. Characterizing heterogeneous viral populations and their evolution by high-throughput sequencin…
View article: Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research
Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research Open
SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causes the infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformat…
View article: Evaluating assembly and variant calling software for strain-resolved analysis of large DNA-viruses
Evaluating assembly and variant calling software for strain-resolved analysis of large DNA-viruses Open
Infection with human cytomegalovirus (HCMV) can cause severe complications in immunocompromised individuals and congenitally infected children. Characterizing heterogeneous viral populations and their evolution by high-throughput sequencin…
View article: Cograph editing: Merging modules is equivalent to editing P_4s
Cograph editing: Merging modules is equivalent to editing P_4s Open
The modular decomposition of a graph G = (V, E) does not contain prime modules if and only if G is a cograph, that is, if no quadruple of vertices induces a simple connected path P4. The cograph editing problem consists in inserting into a…
View article: CAMITAX: Taxon labels for microbial genomes
CAMITAX: Taxon labels for microbial genomes Open
Background The number of microbial genome sequences is increasing exponentially, especially thanks to recent advances in recovering complete or near-complete genomes from metagenomes and single cells. Assigning reliable taxon labels to gen…
View article: Building Field-Based Ecophysiological Genome-to-Phenome Prediction
Building Field-Based Ecophysiological Genome-to-Phenome Prediction Open
Feeding the estimated global population of 9 billion persons by 2050 will require a doubling of the food supply. However, the annual yield\nrates of gain for major grain crops is only one-quarter to one half of that which is necessary to r…
View article: CAMISIM: simulating metagenomes and microbial communities
CAMISIM: simulating metagenomes and microbial communities Open
CAMISIM can simulate a wide variety of microbial communities and metagenome data sets together with standards of truth for method evaluation. All data sets and the software are freely available at https://github.com/CAMI-challenge/CAMISIM.
View article: CAMITAX: Taxon labels for microbial genomes
CAMITAX: Taxon labels for microbial genomes Open
The number of microbial genome sequences is growing exponentially, also thanks to recent advances in recovering complete or near-complete genomes from metagenomes and single cells. Assigning reliable taxon labels to genomes is key and ofte…
View article: AMBER: Assessment of Metagenome BinnERs
AMBER: Assessment of Metagenome BinnERs Open
Reconstructing the genomes of microbial community members is key to the interpretation of shotgun metagenome samples. Genome binning programs deconvolute reads or assembled contigs of such samples into individual bins. However, assessing t…
View article: CAMISIM: Simulating metagenomes and microbial communities
CAMISIM: Simulating metagenomes and microbial communities Open
Shotgun metagenome data sets of microbial communities are highly diverse, not only due to the natural variation of the underlying biological systems, but also due to differences in laboratory protocols, replicate numbers, and sequencing te…
View article: AMBER: Assessment of Metagenome BinnERs
AMBER: Assessment of Metagenome BinnERs Open
Reconstructing the genomes of microbial community members is key to the interpretation of shotgun metagenome samples. Genome binning programs deconvolute reads or assembled contigs of such samples into individual bins, but assessing their …
View article: Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software
Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software Open
Methods for assembly, taxonomic profiling and binning are key to interpreting metagenome data, but a lack of consensus about benchmarking complicates performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) chall…
View article: Cograph Editing: Merging Modules is equivalent to Editing P4's
Cograph Editing: Merging Modules is equivalent to Editing P4's Open
The modular decomposition of a graph $G=(V,E)$ does not contain prime modules if and only if $G$ is a cograph, that is, if no quadruple of vertices induces a simple connected path $P_4$. The cograph editing problem consists in inserting in…
View article: Merging Modules is equivalent to Editing P4's.
Merging Modules is equivalent to Editing P4's. Open
The modular decomposition of a graph $G=(V,E)$ does not contain prime modules if and only if $G$ is a cograph, that is, if no quadruple of vertices induces a simple connected path $P_4$. The cograph editing problem consists in inserting in…
View article: Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software
Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software Open
In metagenome analysis, computational methods for assembly, taxonomic profiling and binning are key components facilitating downstream biological data interpretation. However, a lack of consensus about benchmarking datasets and evaluation …
View article: Techniques for the Cograph Editing Problem: Module Merge is equivalent to Editing P4s
Techniques for the Cograph Editing Problem: Module Merge is equivalent to Editing P4s Open
Cographs are graphs in which no four vertices induce a simple connected path $P_4$. Cograph editing is to find for a given graph $G = (V,E)$ a set of at most $k$ edge additions and deletions that transform $G$ into a cograph. This combinat…
View article: Techniques for the Cograph Editing Problem: Module Merge is equivalent\n to Editing P4s
Techniques for the Cograph Editing Problem: Module Merge is equivalent\n to Editing P4s Open
Cographs are graphs in which no four vertices induce a simple connected path\n$P_4$. Cograph editing is to find for a given graph $G = (V,E)$ a set of at\nmost $k$ edge additions and deletions that transform $G$ into a cograph. This\ncombi…