BOL: Related items

SeqMule: Automated human exome/genome variants detection

Abhimanyu Singh — Tue, 07 Mar 2017 10:12:36 -0600

SeqMule takes single-end or paird-end FASTQ or BAM files, generates a script consisting of more than 10 popular alignment, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its configuration file. SeqMule also has some built-in functions, such as pooling consensus calls from various callers, plotting a Venn diagram showing intersection among different callers, and downloading databases. SeqMule can be used for both Mendelian disease study and cancer genome study.

Address of the bookmark: http://seqmule.openbioinformatics.org/en/latest/

gbtools: Interactive Visualization of Metagenome Bins in R

Jit — Sun, 26 Mar 2017 15:41:31 -0500

We have developed gbtools, a software package that allows users to visualize metagenomic assemblies by plotting coverage (sequencing depth) and GC values of contigs, and also to annotate the plots with taxonomic information. Different sets of annotations, including taxonomic assignments from conserved marker genes or SSU rRNA genes, can be imported simultaneously; users can choose which annotations to plot. Bins can be manually defined from plots, or be imported from third-party binning tools and overlaid onto plots, such that results from different methods can be compared side-by-side. gbtools reports summary statistics of bins including marker gene completeness, and allows the user to add or subtract bins with each other.

Tool at https://github.com/kbseah/genome-bin-tools

Address of the bookmark: http://journal.frontiersin.org/article/10.3389/fmicb.2015.01451/full

Download assemblies from NCBI

Bulbul — Mon, 15 May 2017 06:02:32 -0500

A new “Download assemblies” button is now available in the Assembly database. This makes it easy to download data for multiple genomes without having to write scripts.

For example, you can run a search in Assembly and use check boxes (see left side of screenshot below) to refine the set of genome assemblies of interest. Then, just open the “Download assemblies” menu, choose the source database (GenBank or RefSeq), choose the file type, and start the download. An archive file will be saved to your computer that can be expanded into a folder containing your selected genome data files.

More at https://ncbiinsights.ncbi.nlm.nih.gov/2017/05/08/genome-data-download-made-easy/

CAR: Reconstructing Contiguous Regions of an Ancestral Genome

Abhimanyu Singh — Thu, 18 May 2017 05:24:01 -0500

We describe a new method for predicting the ancestral order and orientation of those intervals from their observed adjacencies in modern species. We combine the results from this method with data from chromosome painting experiments to produce a map of an early mammalian genome that accounts for 96.8% of the available human genome sequence data. The precision is further increased by mapping inversions as small as 31 bp. Analysis of the predicted evolutionary breakpoints in the human lineage confirms certain published observations but disagrees with others. Although only a few mammalian genomes are currently sequenced to high precision, our theoretical analyses and computer simulations indicate that our results are reasonably accurate and that they will become highly accurate in the foreseeable future. Our methods were developed as part of a project to reconstruct the genome sequence of the last ancestor of human, dogs, and most other placental mammals;

Address of the bookmark: http://www.bx.psu.edu/miller_lab/car/

Jvarkit : Java utilities for Bioinformatics

Jit — Fri, 08 Jun 2018 09:31:55 -0500

Collection of Java tool kits for bioinformatics works: Jvarkit : Java utilities for Bioinformatics

Address of the bookmark: http://lindenb.github.io/jvarkit/

Machine learning training and courses in bioinformatics !

Rahul Nayak — Tue, 31 Dec 2019 19:33:07 -0600

Machine learning techniques have been successful in analyzing biological data because of their capabilities in handling randomness and uncertainty of data noise and in generalization. In this class, we will learn basics about probabilistic models and machine learning techniques. We will focus on probabilistic models (Markov models, Hidden Markov models, and Bayesian networks) for biological sequence analysis and systems biology. Other machine learning techniques, such as Naive bayes, neural networks and SVMs will only be covered briefly.

More at http://homes.sice.indiana.edu/yye/lab/teaching/spring2017-I529/

Sequence Ontology Bioinformatics Analysis (SOBA) tool to provide a simple statistical and graphical summary of an annotated genome

BioStar — Wed, 22 Jul 2020 10:11:13 -0500

We have developed the Sequence Ontology Bioinformatics Analysis (SOBA) tool to provide a simple statistical and graphical summary of an annotated genome. We envisage its use during annotation jamborees, genome comparison and for use by developers for rapid feedback during annotation software development and testing. SOBA also provides annotation consistency feedback to ensure correct use of terminology within annotations, and guides users to add new terms to the Sequence Ontology when required. SOBA is available at http://www.sequenceontology.org/cgi-bin/soba.cgi.

More at https://pubmed.ncbi.nlm.nih.gov/20494974/

Address of the bookmark: http://www.sequenceontology.org/cgi-bin/soba.cgi

Bioinformatics Scientist, Production Bioinformatics @ South San Francisco, CA

Thu, 19 Aug 2021 08:45:24 -0500

wist is looking for a Bioinformatics Scientist to join our Production Bioinformatics Team. You will work alongside research scientists, software engineers and data scientists to further deliver on our mission to expand access to best-in-class synthetic biology and next-generation sequencing applications. You will be developing and engineering tools to better evaluate and build hardened, production quality pipelines, optimize data quality, and automate lab and bioinformatics processes. Our ideal candidate is an organized problem solver with a background in developing and building novel production-quality bioinformatics tools and packages. Equally excellent communication skills and a proven ability to work independently are required.

More at https://boards.greenhouse.io/twistbioscience/jobs/3135495?gh_src=9ecc0b941us

Job offer for a postdoctoral researcher in genomics / bioinformatics (2 years)

Fri, 22 Oct 2021 04:44:33 -0500

Ongoing research in the group of Karine Van Doninck involves topics at the core of
evolutionary biology, including the evolution of sex, genome maintenance,
recombination and extreme stress resistance on different eukaryotic systems,
including rotifers, amoeba and Corbicula clams. We are employing different tools
(including experimental ecology, population genetics, phylogeny, comparative
genomics, transcriptomics, bioinformatics, molecular and cellular biology) to study
evolutionary processes at the level of populations, both experimental and natural, and
genomes.

Offer
We offer a full-time contract for two years. The contract starts between October 2021
and December 2021. The position involves no or extremely light teaching load, if the
candidate is interested. Salaries are competitive at the European level. The recruited
person will benefit from the Belgian social insurance scheme (health care, etc.) without
additional expenses.

Profile
Applicants are expected to show outstanding commitment to research and must have
obtained a PhD by the start of the position. A strong expertise in genomics is required.
More specifically, solid competences in bioinformatics (e.g. scripting pipelines) and in
genome evolution are needed. Knowledge or interest regarding recombination,
metazoan evolution, phylogenomics and population genomics is an added-value.

Application
Applications should be submitted via email to karine.van.doninck@ulb.be. The
application package should contain the following documents:
- A curriculum vitae with the complete list of publications
- A cover letter mentioning why the candidate is interested in the position
- Minimum 2 recommendation letters
Interviews: Interviews will be conducted with the selected candidates. Selected
candidates could also be invited to give a seminar to MBE ULB.
For any additional information, please contact karine.van.doninck@ulb.be

Bioinformatics Tutorial !

Neel — Mon, 22 Aug 2022 23:56:22 -0500

This site aims to be a useful resource for bioinformatics beginners. Feel free to jump right in with the section most relevant to you, and if you're not sure, then the place to start is definitely Unix

Address of the bookmark: https://astrobiomike.github.io/