To understand the impact of gut microbes on human health and well-being it is crucial to
assess their genetic potential. Here we describe the Illumina-based metagenomic sequencing, …

Background There is a rapidly increasing amount of de novo genome assembly using next-generation
sequencing (NGS) short reads; however, several big challenges remain to be …

Insects are the most speciose group of animals, but the phylogenetic relationships of many
major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-…

The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically
poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the …

Optogenetic tools enable examination of how specific cell types contribute to brain circuit
functions. A long-standing question is whether it is possible to independently activate two …

Motivation: Transcriptome sequencing has long been the favored method for quickly and
inexpensively obtaining a large number of gene sequences from an organism with no …

Low-cost short read sequencing technology has revolutionized genomics, though it is only
just becoming practical for the high-quality de novo assembly of a novel large genome. We …

After the publication of ‘SOAPdenovo2: an empirically improved memory-efficient short-read
de novo assembler. GigaScience 2012 1: 18’[1] this paper was used as case study by the …

Motivation: The boost of next-generation sequencing technologies provides us with an
unprecedented opportunity for elucidating genetic mysteries, yet the short-read length hinders us …

Many phylogenomic studies based on transcriptomes have been limited to “single-copy”
genes due to methodological challenges in homology and orthology inferences. Only a …