We introduce Grinder (http://sourceforge.net/projects/biogrinder/), an open-source bioinformatic tool to simulate amplicon and shotgun (genomic, metagenomic, transcriptomic and metatranscriptomic) datasets from reference sequences. This is the first tool to simulate amplicon datasets (e.g. 16S rRNA) widely used by microbial ecologists. Grinder can create sequence libraries with a specific community structure, α and β diversities and experimental biases (e.g. chimeras, gene copy number variation) for commonly used sequencing platforms. This versatility allows the creation of simple to complex read datasets necessary for hypothesis testing when developing bioinformatic software, benchmarking existing tools or designing sequence-based experiments. Grinder is particularly useful for simulating clinical or environmental microbial communities and complements the use of in vitro mock communities.
The frequency of chimeric molecules as a consequence of PCR co-amplification of 16S rRNA genes from different bacterial species
Understanding bias in microbial community analysis techniques due to rrn operon copy number heterogeneity
Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data
Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates
The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes
Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins
A novel single cDNA amplicon pyrosequencing method for high-throughput, cost-effective sequence-based HLA class I genotyping
Assessment of viral community functional potential from viral metagenomes may be hampered by contamination with cellular sequences
Beyond classification: gene-family phylogenies from shotgun metagenomic reads enable accurate community analysis
Comparison of DNA extraction methods for microbial community profiling with an application to pediatric bronchoalveolar lavage samples
Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products
CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction
Enhancing the detection of barcoded reads in high throughput DNA sequencing data by controlling the false discovery rate
The effects of read length, quality and quantity on microsatellite discovery and primer development: from Illumina to PacBio
Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome
ViQuaS: an improved reconstruction pipeline for viral quasispecies spectra generated by next-generation sequencing
Don't put all your eggs in one basket: a cost-effective and powerful method to optimize primer choice for rRNA environmental community analyses using the Fluidigm Access Array
Metabarcoding of Fecal Samples to Determine Herbivore Diets: A Case Study of the Endangered Pacific Pocket Mouse
The utility of DNA metabarcoding for studying the response of arthropod diversity and composition to land-use change in the tropics
Analysis of large 16S rRNA Illumina data sets: Impact of singleton read filtering on microbial community description
SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution
MetaPalette: a k -mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation
Assessing viral taxonomic composition in benthic marine ecosystems: reliability and efficiency of different bioinformatic tools for viral metagenomic analyses
Reconstruction of plasmids by shotgun sequencing from environmental DNA: which bioinformatic workflow?
Systematic review of next-generation sequencing simulators: computational tools, features and perspectives
ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores
Biochemical Characteristics of Microbial Enzymes and Their Significance from Industrial Perspectives
Analysis of sequencing strategies and tools for taxonomic annotation: Defining standards for progressive metagenomics
Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies
Review, Evaluation, and Directions for Gene-Targeted Assembly for Ecological Analyses of Metagenomes
Wide spectrum and high frequency of genomic structural variation, including transposable elements, in large double-stranded DNA viruses
CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data.
SimuSCoP: reliably simulate Illumina sequencing data based on position and context dependent profiles
MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples
Data-Driven Modeling for Species-Level Taxonomic Assignment From 16S rRNA: Application to Human Microbiomes
Diel transcriptional oscillations of light-sensitive regulatory elements in open-ocean eukaryotic plankton communities.
Daring to be differential: metabarcoding analysis of soil and plant-related microbial communities using amplicon sequence variants and operational taxonomical units
Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.
Neural Activity: Imaging
Imaging of neural activity in vivo has developed rapidly recently with the advancement of fluorescence microscopy, including new applications using miniaturized microscopes (miniscopes). This feed follows the progress in this growing field.
The Tendon Seed Network
Tendons are rich in the extracellular matrix and are abundant throughout the body providing essential roles including structure and mobility. The transcriptome of tendons is being compiled to understand the micro-anatomical functioning of tendons. Discover the latest research pertaining to the Tendon Seed Network here.
Myocardial stunning is a mechanical dysfunction that persists after reperfusion of previously ischemic tissue in the absence of irreversible damage including myocardial necrosis. Here is the latest research.
Chronic Fatigue Syndrome
Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.
Incretins are metabolic hormones that stimulate a decrease in glucose levels in the blood and they have been implicated in glycemic regulation in the remission phase of type 1 diabetes. Here is the latest research.
Chromatin Regulation and Circadian Clocks
The circadian clock plays an important role in regulating transcriptional dynamics through changes in chromatin folding and remodelling. Discover the latest research on Chromatin Regulation and Circadian Clocks here.
“Long Covid-19” describes illness in patients who are reporting long-lasting effects of the SARS-CoV-19 infection, often long after they have recovered from acute Covid-19. Ongoing health issues often reported include low exercise tolerance and breathing difficulties, chronic tiredness, and mental health problems such as post-traumatic stress disorder and depression. This feed follows the latest research into Long Covid.
Spatio-Temporal Regulation of DNA Repair
DNA repair is a complex process regulated by several different classes of enzymes, including ligases, endonucleases, and polymerases. This feed focuses on the spatial and temporal regulation that accompanies DNA damage signaling and repair enzymes and processes.