Though the specific implementation of the idea of the rectangle graph approach is already included into the current SPAdes distribution, we're also releasing the Rectangle Graph Module (RGM) as the separate code which can be run independently of SPAdes. Although RGM differs from the current implementation of the rectangle graph approach in SPAdes, in the future we plan to integrate RGM in SPAdes. RGM can be run with other genome assemblers if they use the graph format as SPAdes files.

For more details see: Nikolay Vyahhi, Son K. Pham, Pavel Pevzner. From de Bruijn Graphs to Rectangle Graphs for Genome Assembly, Lecture Notes in Bioinformatics 7534 (2012), pp. 249-261.

Address of the bookmark: http://bioinf.spbau.ru/en/rectangles

The assembly process can be summarized as follows:

1. overlap
2. patch reads
3. overlap (again)
4. scrubbing
5. assembly graph construction and touring
6. optional read correction
7. fasta file creation

Address of the bookmark: https://github.com/schloi/MARVEL

Address of the bookmark: http://www.zhanyuwang.xin/wordpress/index.php/2017/07/21/baum-improving-genome-assembly-by-adaptive-unique-mapping-and-local-overlap-layout-consensus/

RaGOO is a tool for coalescing genome assembly contigs into pseudochromosomes via minimap2 alignments to a closely related reference genome. The focus of this tool is on practicality and therefore has the following features:

1. Good performance. On a MacBook Pro using Arabidopsis data, pseudochromosome construction takes less than a minute and the whole pipeline with SV calling takes ~2 minutes.
2. Intact ordering and orienting of contigs.
3. Misassembly correction
4. GFF lift-over
5. Structural variant calling with and integrated version of Assemblytics
6. Confidence scores associated with the grouping, localization, and orientation for each contig.

Address of the bookmark: https://github.com/malonge/RaGOO

Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools.

Commonly used biological software and example script files for different assembly pipelines have also been provided, where the example script files can be updated to suit one’s experimental needs. Genobuntu attempts to reduce the amount of time and energy needed to build software workstations and it can also act as a good teaching source for a class room setting.

Therefore, Genobuntu offers a well-tailored environment for both novices and experts working in the field of genome assembly.

Address of the bookmark: https://sourceforge.net/projects/genobuntu/

Address of the bookmark: https://github.com/sc932/ALE

Searcg link https://metagraph.ethz.ch/search 

Pre-print https://www.biorxiv.org/content/10.1101/2020.10.01.322164v4 

Address of the bookmark: https://metagraph.ethz.ch/

The postdocs will join an international group and network of researchers at the University of Vienna studying a diverse range of species and questions in molecular evolution, development, morphology and genomics. Our group is also part of the large evolVienna network of more than 50 evolutionary biology labs in Vienna, across several universities and research institutes. Our Faculty will be relocating to a new campus at the Vienna Biocenter in summer 2021 (https://biologiezentrum.univie.ac.at/en/). Vienna is a vibrant historic European capital with a high QOL. Information about postdoctoral salaries in Austria can be found on this webpage: https://www.fwf.ac.at/en/research-funding/personnel-costs/

Earliest start date will be after July 2021. Initial term of employment is for two years with the possibility of extension. Remote working, at least initially, is a possibility.

Requirements:
- PhD degree or equivalent by the start date
- Publishing record in peer-reviewed journals or evidence thereof
- At least 2 letters of support

Applications including a letter of motivation should be submitted via the Job Center to the University of Vienna (https://personalwesen.univie.ac.at/en/jobs-recruiting/job-center/,
job reference number 11615).

Application deadline: January 15th 2021.
Application link: https://univis.univie.ac.at/ebewerbung

In addition to the knowledge of the human genome, all these genomes, widely sampled across mammals, can be used to research how particular organisms respond to different conditions. Some otters, for example, have a thick, water-resistant shell, and some rodents, but not all, have adapted to hibernation. These animal traits will help us to understand human traits, such as metabolic diseases.

With climate change and more animal ecosystems being threatened by human activity, the protection of endangered species is becoming increasingly important. Scientists have historically researched several people in various populations of a species to understand the genetic variation that occurs in that species. This is important for understanding how particular species can be protected. In this study, animals on the Red List of Endangered Species of the International Union for Conservation of Nature had fewer differences in their genomes, which is consistent with their endangered status.

Ref @ A comparative genomics multitool for scientific discovery and conservation https://www.nature.com/articles/s41586-020-2876-6

 Data at http://zoonomiaproject.org/

We are looking for a highly motivated candidate with a PhD degree in
Bioinformatics or a related field. Candidates are expected to have a
strong background in evolutionary biology and/or comparative functional
genomics. Additional experiences in single cell functional genomics
analyses, statistics and computational data analyses are a plus, as is
an interest in comparative developmental (EvoDevo) questions.

We offer a dynamic and interactive research environment with state-of-the
art research facilities, good research funding and internationally
competitive salaries.

The Tschopp lab (www.evolution.unibas.ch/tschopp/research/)
studies the gene regulatory mechanisms of cell type
specification and evolution in vertebrates. See also our
preprints at https://doi.org/10.1101/2024.03.26.586769 and
https://doi.org/10.1101/2024.11.28.625862 Applications should include
a motivation letter, a CV, a list of publications, a statement about
research interests, as well as the names and contact details of at
least two referees. Applications (in the form of a single .pdf file)
should be sent to Patrick Tschopp (patrick.tschopp@unibas.ch); review
of applications will begin on January 1st 2025, and will continue until
the position is filled.

Patrick Tschopp