[Experimental] List of manuscripts available for review volunteers
1 manuscript available for review volunteers
September 20, 2017
Exogenous sequence contamination presents a challenge in first-draft genomes because it can lead to non-contiguous, chimeric assembled sequences. This can mislead downstream analyses reliant on synteny, such as linkage-based analyses. Recently, the Mojave Desert Tortoise (Gopherus agassizii) draft genome was published as a resource to advance conservation efforts for the threatened species and discover more about chelonian biology and evolution. Here, we illustrate steps taken to improve the desert tortoise draft genome by removing contaminating sequences—actions that are typically carried out after the initial release of a draft genome assembly. We used information from NCBI’s Vecscreen output to remove intra-scaffold contamination and trim heading and trailing Ns. We then reordered and renamed scaffolds, and transferred the gene annotation onto this assembly. Finally, we describe the tools developed for this pipeline, freely available on Github (https://github.com/thw17/G_agassizii_reference_update), which facilitate post-assembly processing of other draft genomes. The new gopAga1.1 genome has an N50 of 251 KB, L50 of 2592 scaffolds, and its annotation retains 17,201 of the original 20,172 genes that were unaffected by the scaffold processing.

FAQs

Is this open peer review?

No, peer review is still single-blind and all recommendations are private between the authors and Academic Editor. However, any reviewer has the option to sign their report, and once accepted for publication then that review can be shown publicly - again this is optional.

Will I be guaranteed to review if I volunteer?

No. Volunteering is not a guarantee that you will be asked to review. This is for many reasons. For one, reviewers must have relevant qualifications for any manuscript and void of any conflicts of interest. Additionally, it could be that enough reviewers have accepted an invitation to review already, in which case we would not invite any more.

Why aren't there more manuscripts available?

Manuscripts are shown when authors have opted-in for obtaining reviewers through the reviewer-match service. Additionally, there may already be enough reviewers found through other means, for example, invitations sent by the Academic Editor in charge.

What are the editorial criteria?

Please visit the editorial criteria page for initial guidance. You will also be given additional information if invited to review.