Microbiome research has grown rapidly over the past decade, with a proliferation of new
methods that seek to make sense of large, complex data sets. Here, we survey two of the …

Environmental DNA sequencing has revealed the expansive biodiversity of microorganisms
and clarified the relationship between host-associated microbial communities and host …

It is increasingly necessary for researchers in all fields to write computer code, and in order
to reproduce research results, it is important that this code is published. We present Jupyter …

Open access, open data, open source and other open scholarship practices are growing in
popularity and necessity. However, widespread adoption of these practices has not yet been …

Advances in high-throughput sequencing and 'omics technologies are revolutionizing
studies of naturally occurring microbial communities. Comprehensive investigations of …

De novo assembly of RNA-seq data enables researchers to study transcriptomes without the
need for a genome sequence; this approach can be usefully applied, for instance, in …

Next generation sequencing has made it possible to perform differential gene expression
studies in non-model organisms. For these studies, the need for a reference genome is …

Motivation: Today, the base code of DNA is mostly determined through sequencing by
synthesis as provided by the Illumina sequencers. Although highly accurate, resulting reads …

Ctenophora, comprising approximately 200 described species, is an important lineage for
understanding metazoan evolution and is of great ecological and economic importance …

The khmer package is a freely available software library for working efficiently with fixed
length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer …