JBrowse 2: a modular genome browser with views of synteny and structural variation.

We present JBrowse 2, a general-purpose genome annotation browser offering enhanced visualization of complex structural variation and evolutionary relationships. It retains core features of JBrowse while adding new views for synteny, dotplots, breakpoints, gene fusions, and whole-genome overviews. It allows users to share sessions, open multiple genomes, and navigate between views. It can be embedded in a web page, used as a standalone application, or run from Jupyter notebooks or R sessions. These improvements are enabled by a ground-up redesign using modern web technology. We describe application functionality, use cases, performance benchmarks, and implementation notes for web administrators and developers.

JBrowse Jupyter: a Python interface to JBrowse 2.

MOTIVATION: JBrowse Jupyter is a package that aims to close the gap between Python programming and genomic visualization. Web-based genome browsers are routinely used for publishing and inspecting genome annotations. Historically they have been deployed at the end of bioinformatics pipelines, typically decoupled from the analysis itself. However, emerging technologies such as Jupyter notebooks enable a more rapid iterative cycle of development, analysis and visualization. RESULTS: We have developed a package that provides a Python interface to JBrowse 2's suite of embeddable components, including the primary Linear Genome View. The package enables users to quickly set up, launch and customize JBrowse views from Jupyter notebooks. In addition, users can share their data via Google's Colab notebooks, providing reproducible interactive views. AVAILABILITY AND IMPLEMENTATION: JBrowse Jupyter is released under the Apache License and is available for download on PyPI. Source code and demos are available on GitHub at https://github.com/GMOD/jbrowse-jupyter.

Reproductive outcomes after surgical treatment of asherman syndrome: A systematic review.

In this systematic review, we analysed the reproductive outcomes of hysteroscopic adhesiolysis in women with Asherman syndrome (AS). We searched PubMed, Web of Science and Cochrane Library (from database inception to April 2018) and selected studies that quantitatively described the reproductive outcomes. We assessed study quality and pooled rate data for each outcome. There were 54 studies (4640 women) of varying quality. The pooled rate of pregnancy was 50.7% (95% CI [confidence interval]: 49.1 to 52.3) in 53 studies, early pregnancy loss was 17.7% (95% CI: 15.9 to 19.6) in 31 studies, ectopic pregnancy (EP) was 4.2% (95% CI: 2.8 to 6.3) in 9 studies, mid-trimester loss (MTL) was 11.5% (95% CI: 7.6 to 17.8) in 7 studies, cervical incompetence was 12.5% (95% CI: 3.3 to 33.5) in 2 studies and placenta accreta syndrome was 10.1% (95% CI: 8.6 to 11.8) in 23 studies. The pregnancy rate in women with severe adhesion was significantly lower than that in women with mild adhesion (P = 0.021). These results can be used to counsel women with AS before surgical treatment and for planning antenatal care after conception.