BOL: All site bookmarks

CViT: Chromosome Viewing Tool

Rahul Nayak — Wed, 02 Jan 2019 04:10:09 -0600

CViT - Chromosome Viewing Tool. A collection of Perl scripts that enable quick visualizations of features on linkage groups, psuedochromosomes or cytogenetic maps. Intended for whole-genome views of data but can be used to create images of single chromosomes/linkage groups, contigs, or BACs, or even proteins -- any feature that has a location on a backbone. Handles most standard genetic/genomic coordinate systems. Reads GFF3 data and produces a PNG or SVG image.

https://www.hindawi.com/journals/ijpg/2011/373875/

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

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/

GenoViz: Visualization software for genomics

Rahul Nayak — Wed, 02 Jan 2019 04:07:57 -0600

GenoViz provides software applications and re-usable components for data visualization and data sharing in genomics. Our flagship product is Integrated Genome Browser (IGB).

For more information about IGB, visit http://bioviz.org.

Source code for the project was hosted here for many years. In 2014, we moved to a new git repository at http://www.bitbucket.org/lorainelab/integrated-genome-browser. We are still using SourceForge to distribute new releases of IGB as compiled code (igb.zip) you can use to run IGB on your computer.

If you have questions, feel free to get in touch. Contact project head Ann Loraine (aloraine@uncc.edu) or lead developer David Norris (dcnorris@uncc.edu>).

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

HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning

Abhimanyu Singh — Tue, 01 Jan 2019 12:01:00 -0600

HECIL—Hybrid Error Correction with Iterative Learning—a hybrid error correction framework that determines a correction policy for erroneous long reads, based on optimal combinations of decision weights obtained from short read alignments.

HECIL’s core algorithm by introducing an iterative learning paradigm that enhances the correction policy at each iteration by incorporating knowledge gathered from previous iterations via data-driven confidence metrics assigned to prior corrections.

Address of the bookmark: https://github.com/NDBL/HECIL

Hawkeye: an interactive visual analytics tool for genome assemblies

Abhimanyu Singh — Tue, 01 Jan 2019 11:56:17 -0600

Genome sequencing remains an inexact science, and genome sequences can contain significant errors if they are not carefully examined. Hawkeye is our new visual analytics tool for genome assemblies, designed to aid in identifying and correcting assembly errors. Users can analyze all levels of an assembly along with summary statistics and assembly metrics, and are guided by a ranking component towards likely mis-assemblies. Hawkeye is freely available and released as part of the open source AMOS project http://amos.sourceforge.net/hawkeye.

https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-3-r34

Address of the bookmark: http://amos.sourceforge.net/wiki/index.php?title=Hawkeye

Reactome Pathway Database

BioStar — Mon, 31 Dec 2018 02:41:33 -0600

REACTOME is an open-source, open access, manually curated and peer-reviewed pathway database. Our goal is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge to support basic and clinical research, genome analysis, modeling, systems biology and education. Founded in 2003, the Reactome project is led by Lincoln Stein of OICR, Peter D’Eustachio of NYULMC, Henning Hermjakob of EMBL-EBI, and Guanming Wu of OHSU.

Address of the bookmark: https://reactome.org/

GeneOverlap: An R package to test and visualize gene overlaps

Jit — Thu, 27 Dec 2018 19:45:52 -0600

Overlapping gene lists can reveal biological meanings and may lead to novel hypotheses. For example, histone modification is an important cellular mechanism that can pack and re-pack chromatin. By making the chromatin structure more dense or loose, the gene expression can be turned on or off. Tri-methylation on lysine 4 of histone H3 (H3K4me3) is associated with gene activation and its genome-wide enrichment can be mapped by using ChIP-seq experiments. Because of its activating role, if we overlap the genes that are bound by H3K4me3 with the genes that are highly expressed, we should expect a positive association. Similary, we can perform such kind of overlapping between the gene lists of different histone modifications with that of various expression groups and establish each histone modification’s role in gene regulation.

Address of the bookmark: https://bioconductor.org/packages/release/bioc/vignettes/GeneOverlap/inst/doc/GeneOverlap.pdf

NanoPack: visualizing and processing long-read sequencing data

Jit — Tue, 25 Dec 2018 21:20:50 -0600

The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are compatible with Linux, Mac OS and the MS Windows 10 subsystem for Linux and are available as a graphical user interface, a web service at http://nanoplot.bioinf.be and command line tools.

Address of the bookmark: https://github.com/wdecoster/nanopack

Versatile genome assembly evaluation with QUAST-LG

Jit — Fri, 21 Dec 2018 22:06:31 -0600

QUAST-LG is an extension of QUAST intended for evaluating large-scale genome assemblies (up to mammalian-size).

QUAST-LG is included in the QUAST package starting from version 5.0.0 (download the latest release). Run QUAST as usual and do not forget to add ‐‐large option to your command!

A short list of the new features (see CHANGES for all):

Significant speedup achieved by both use of new fast aligner (minimap2) and the refactoring of alignment analyzing modules
New k-mer-based completeness and correctness metrics
BUSCO added for enhanced reference-free analysis
The concept of upper bound assembly (theoretical limits on the assembly completeness and contiguity for a given genome and set of reads)

Address of the bookmark: http://cab.spbu.ru/software/quast-lg/

Genome Annotation using MAKER tutorial !

Shruti Paniwala — Thu, 20 Dec 2018 17:39:23 -0600

MAKER is a great tool for annotating a reference genome using empirical and ab initiogene predictions. GMOD, the umbrella organization that includes MAKER, has some nice tutorials online for running MAKER. However, these were quite simplified examples and it took a bit of effort to wrap my head completely around everything. Here I will describe a de novo genome annotation for Boa constrictor in detail, so that there is a record and that it is easy to use this as a guide to annotate any genome.

Address of the bookmark: https://www.biostars.org/p/261203/