Shotgun metagenomics, from sampling to analysis
Diverse microbial communities of bacteria, archaea, viruses and single-celled eukaryotes
have crucial roles in the environment and in human health. However, microbes are …
have crucial roles in the environment and in human health. However, microbes are …
Piercing the dark matter: bioinformatics of long-range sequencing and mapping
Several new genomics technologies have become available that offer long-read sequencing
or long-range mapping with higher throughput and higher resolution analysis than ever …
or long-range mapping with higher throughput and higher resolution analysis than ever …
Towards complete and error-free genome assemblies of all vertebrate species
High-quality and complete reference genome assemblies are fundamental for the
application of genomics to biology, disease, and biodiversity conservation. However, such …
application of genomics to biology, disease, and biodiversity conservation. However, such …
Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes
K Shafin, T Pesout, R Lorig-Roach, M Haukness… - Nature …, 2020 - nature.com
De novo assembly of a human genome using nanopore long-read sequences has been
reported, but it used more than 150,000 CPU hours and weeks of wall-clock time. To enable …
reported, but it used more than 150,000 CPU hours and weeks of wall-clock time. To enable …
Versatile genome assembly evaluation with QUAST-LG
Motivation The emergence of high-throughput sequencing technologies revolutionized
genomics in early 2000s. The next revolution came with the era of long-read sequencing …
genomics in early 2000s. The next revolution came with the era of long-read sequencing …
High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development
Using the latest sequencing and optical mapping technologies, we have produced a high-
quality de novo assembly of the apple (Malus domestica Borkh.) genome. Repeat …
quality de novo assembly of the apple (Malus domestica Borkh.) genome. Repeat …
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly
VA Schneider, T Graves-Lindsay, K Howe… - Genome …, 2017 - genome.cshlp.org
The human reference genome assembly plays a central role in nearly all aspects of today's
basic and clinical research. GRCh38 is the first coordinate-changing assembly update since …
basic and clinical research. GRCh38 is the first coordinate-changing assembly update since …
Assessing genome assembly quality using the LTR Assembly Index (LAI)
Assembling a plant genome is challenging due to the abundance of repetitive sequences,
yet no standard is available to evaluate the assembly of repeat space. LTR retrotransposons …
yet no standard is available to evaluate the assembly of repeat space. LTR retrotransposons …
Finding the genomic basis of local adaptation: pitfalls, practical solutions, and future directions
Uncovering the genetic and evolutionary basis of local adaptation is a major focus of
evolutionary biology. The recent development of cost-effective methods for obtaining high …
evolutionary biology. The recent development of cost-effective methods for obtaining high …
Parallel evolution of cannabinoid biosynthesis
Modulation of the endocannabinoid system is projected to have therapeutic potential in
almost all human diseases. Accordingly, the high demand for novel cannabinoids stimulates …
almost all human diseases. Accordingly, the high demand for novel cannabinoids stimulates …