Sidebar

Last updated 4 months ago

Clicking the sidebar menu sidebarmenu will open a dropdown with six buttons:

sidebar

Browse

Browse has all filtering related options that allow the user to make custom selections and highlights on both nodes and links.

Import results

Import results has a series of options that allow the user to import JSON files from pATLASflow. Further instructions are provided in the "How to run" sections of the desired Import option.

Statistics

Statistics allows to calculate the desired statistics (e.g. taxa, resistance genes or length) and plot them in a chart.

Projects

Projects has two buttons, one for exporting and another for importing projects. This module provides an easy and rapid way for users to share results, save a current session or load a previously saved session.

Need help?

Documentation

Documentation will open this gitbook.

Video tutorial

Video tutorial will open a popup with a playlist of short tutorials that display pATLAS key features.

FAQs

A set of questions that may occur to users when using pATLAS.

Report sequence.

Here users can report any problem that they find with a plasmid available in pATLAS. For instance, if there is a gene sequence rather than a plasmid. This is part of the crowd curation of pATLAS, which is an initiative that aims to ease the curation of the database by users that find an issue with a RefSeq sequence that shouldn't be a plasmid. pATLAS already has some filters that prevent non-plasmid sequences from getting into the database, however in each database update it is expected that new issues may arise, thus we acknowledge every contribution to help us curate the database.

When clicked, this button will open a pre-formatted GitHub issue like the one below:

The user reporting will have to replace <brief title of the issue> with the desired title and then the body of the issue is already pre-filled with two headers:

  • Sequences accessions - In which the users should state the accession numbers of the sequences that have issues.

  • Description of the issue - Here the users should state the reason by which the sequence should be removed/curated from the pATLAS plasmid database.

About

About contains a brief description of pATLAS and contributions for the development of the tool.