Large-scale quality assessment of prokaryotic genomes with metashot/prok-quality

Metagenomic sequencing allows large-scale identification and genomic characterization. Binning is the process of recovering genomes from complex mixtures of sequence fragments (metagenome contigs) of unknown bacteria and archaeal species. Assessing the quality of genomes recovered from metagenomes requires the use of complex pipelines involving many independent steps, often difficult to reproduce and maintain. A comprehensive, automated and easy-to-use computational workflow for the quality assessment of draft prokaryotic genomes, based on container technology, would greatly improve reproducibility and reusability of published results. We present metashot/prok-quality, a container-enabled Nextflow pipeline for quality assessment and genome dereplication. The metashot/prok-quality tool produces genome quality reports that are compliant with the Minimum Information about a Metagenome-Assembled Genome (MIMAG) standard, and can run out-of-the-box on any platform that supports Nextflow, Docker or Singularity, including computing clusters or batch infrastructures in the cloud. metashot/prok-quality is part of the metashot collection of analysis pipelines. Workflow and documentation are available under GPL3 licence on GitHub.

To Trim or Not to Trim: Effects of Read Trimming on the De Novo Genome Assembly of a Widespread East Asian Passerine, the Rufous-Capped Babbler (Cyanoderma ruficeps Blyth)

Trimming low quality bases from sequencing reads is considered as routine procedure for genome assembly; however, we know little about its pros and cons. Here, we used empirical data to examine how read trimming affects assembled genome quality and computational time for a widespread East Asian passerine, the rufous-capped babbler (Cyanoderma ruficeps Blyth). We found that scaffolds assembled from raw reads were always longer than those from trimmed ones, whereas computational times for the former were sometimes much longer than the latter. Nevertheless, assembly completeness showed little difference among the trimming strategies. One should determine the optimal trimming strategy based on what the assembled genome will be used for. For example, to identify single nucleotide polymorphisms (SNPs) associated with phenotypic evolution, applying PLATANUS to gently trim reads would yield a reference genome with a slightly shorter scaffold length (N50 = 15.64 vs. 16.89 Mb) than the raw reads, but would save 75% of computational time. We also found that chromosomes Z, W, and 4A of the rufous-capped babbler were poorly assembled, likely due to a recently fused, neo-sex chromosome. The rufous-capped babbler genome with long scaffolds and quality gene annotation can provide a good system to study avian ecological adaptation in East Asia.

Reconstructing each cell's genome within complex microbial communities-dream or reality?

As the vast majority of microorganisms have yet to be cultivated in a laboratory setting, access to their genetic makeup has largely been limited to cultivation-independent methods. These methods, namely metagenomics and more recently single-cell genomics, have become cornerstones for microbial ecology and environmental microbiology. One ultimate goal is the recovery of genome sequences from each cell within an environment to move toward a better understanding of community metabolic potential and to provide substrate for experimental work. As single-cell sequencing has the ability to decipher all sequence information contained in an individual cell, this method holds great promise in tackling such challenge. Methodological limitations and inherent biases however do exist, which will be discussed here based on environmental and benchmark data, to assess how far we are from reaching this goal.