BOL: Related items

GenomeView: genome browser and annotation editor

Rahul Nayak — Wed, 02 Jan 2019 04:09:06 -0600

GenomeView is a genome browser and annotation editor that displays reference sequence, annotation, multiple alignments, short read alignments and graphs. Most major data formats are supported. Local and internet files can be loaded.
This project has moved to GitHub: https://github.com/GenomeView/genomeview

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

The Rogers Lab

Mon, 15 Jul 2019 08:07:44 -0500

The Rogers lab studies evolution of genome structure. We explore the ways that complex mutations like duplications, deletions, rearrangements, and retrogenes can create new genetic material. We study how these new mutations are important for adaptation. We are currently working on projects in Drosophila, Mammoths, Elephants, Bivalves, and Frogs absolutely no amphibians. This multi-organism approach can help us understand when and why complex mutations are important for organism fitness.

More at http://evolscientist.com/

ALF--a simulation framework for genome evolution.

Jit — Tue, 22 Oct 2019 22:05:58 -0500

Artificial Life Framework (ALF) simulates a root genome into a number of related genomes. Result files include the resulting gene sequences, true tree and true MSAs. A description of ALF can be found in the following article:

Daniel A Dalquen, Maria Anisimova, Gaston H Gonnet, Christophe Dessimoz: ALF - A Simulation Framework for Genome Evolution. Mol Biol Evol, 29(4):1115-1123, April 2012.
http://mbe.oxfordjournals.org/content/29/4/1115

Address of the bookmark: http://alfsim.org/#index

SeqMule: Automated human exome/genome variants detection

BioStar — Tue, 18 Feb 2020 03:22:54 -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.

Address of the bookmark: https://doc-openbio.readthedocs.io/projects/seqmule/en/latest/

Svardal lab

Sat, 20 Feb 2021 10:01:19 -0600

In the Svardal lab they are interested how the astonishing natural diversity we see on earth came into being, by which forces it formed and how it is changing today. Hence, they are trying to understand the process of evolution, with mathematical models and through the analysis of genome sequencing data.

Genomes, and in particular differences between them, are a crucial source of information to understand evolution and biology in general. They provide a record of the evolutionary past of populations, their relatedness patterns, their demography, and their adaptations.

More at https://www.uantwerpen.be/en/staff/hannes-svardal/svardal-lab/

Calling variants in non-diploid systems

Neel — Sat, 26 Jun 2021 15:37:49 -0500

The main challenge associated with non-diploid variant calling is the difficulty in distinguishing between the sequencing noise (abundant in all NGS platforms) and true low frequency variants. Some of the early attempts to do this well have been accomplished on human mitochondrial DNA although the same approaches will work equally good on viral and bacterial genomes (Rebolledo-Jaramillo et al. 2014, Li et al. 2015).

Address of the bookmark: https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/non-dip/tutorial.html

GenomeTools: The versatile open source genome analysis software

Neel — Wed, 02 Feb 2022 04:00:21 -0600

The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named “libgenometools” which consists of several modules.

If you are interested in gene prediction, have a look at GenomeThreader.

http://genometools.org/pub/

Address of the bookmark: http://genometools.org/

PLAR: Pipeline for lncRNA annotation from RNA-seq data

Abhi — Fri, 07 Jan 2022 06:18:01 -0600

Due to several requests, we are releasing an assingment of orthologs, determined using the same methods used in Hezroni et al. (BLAST, Whole Genome Alignment (WGA), and synteny). One is comparing human GENCODE genes (from GENCODE v30) to lncRNAs from other species identified by PLAR. Available here.

Species	Assembly	Code	Transcriptome	lncRNAs	Protein-coding
Human	hg19	hg19	Download	Download	Download
Rhesus	rheMac3	rm3	Download	Download	Download
Marmoset	calJac3	cj3	Download	Download	Download
Mouse	mm9	mm9	Download	Download	Download
Rabbit	oryCun2	oc2	Download	Download	Download
Dog	canFam3	cf3	Download	Download	Download
Ferret	musFur1	oa3	Download	Download	Download
Opossum	monDom5	md5	Download	Download	Download
Chicken	galGal4	gg4	Download	Download	Download
Lizard	anoCar2	ac2	Download	Download	Download
Coelacanth	latCha1	lc1	Download	Download	Download
Zebrafish	danRer7	dr7	Download	Download	Download
Stickleback	gasAcu1	ga1	Download	Download	Download
Nile tilapia	oreNil2	ot2	Download	Download	Download
Spotted gar	lepOcu1	lo1	Download	Download	Download
Elephant shark	calMil1	cm1	Download	Download	Download
Sea urchin	strPur4	sp4	Download	Download	Download

Address of the bookmark: http://www.weizmann.ac.il/Biological_Regulation/IgorUlitsky/PLAR

The complete sequence of a human genome

Neel — Thu, 31 Mar 2022 23:58:18 -0500

The completed regions include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies.

Address of the bookmark: https://www.science.org/doi/10.1126/science.abj6987

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

Abhi — Tue, 25 Apr 2023 20:58:52 -0500

igvjs - a create-react-app with igv package from npm installed. the igv.js is instrumented to output "DONE" to the console when finished, and to have an increased fetchSizeLimit (which is otherwise git in CRAM longread tests)
jb2-web - stock instance of jbrowse-web v1.7.5
jb1 - stock instance of jbrowse 1 v1.16.11
jb2 embedded - a create-react-app with @jbrowse/react-linear-genome-view

Address of the bookmark: https://github.com/GMOD/jb2profile