BOL: Related items

Harvest: a suite of core-genome alignment and visualization tools

Jit — Fri, 08 Dec 2017 07:16:03 -0600

Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes, including variant calls, recombination detection, and phylogenetic trees.

Tools

Parsnp - Core-genome alignment and analysis
Gingr - Interactive visualization of alignments, trees and variants
HarvestTools - Archiving and postprocessing

Address of the bookmark: https://harvest.readthedocs.io/en/latest/

Tallymer: method to compute K-mer frequencies and its application to annotate large repetitive plant genomes

Jit — Thu, 15 Feb 2018 10:21:02 -0600

Tallymer is based on enhanced suffix arrays. This gives a much larger flexibility concerning the choice of the k-mer size. Tallymer can process large data sizes of several billion bases. We used it in a variety of applications to study the genomes of maize and other plant species. In particular, Tallymer was used to index a set whole genome shotgun sequences from maize (B73) (total size 10⁹ bp).
Tallymer was effective in a variety of applications to aid genome annotation in maize, despite limitations imposed by the relatively low coverage of sequence available.

A manual can be found here.

Address of the bookmark: https://www.zbh.uni-hamburg.de/forschung/arbeitsgruppe-genominformatik/software/tallymer.html

GenomeMapper: Simultaneous alignment of short reads against multiple genomes

Jit — Fri, 25 May 2018 09:29:44 -0500

GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be used to align against multiple genomes simulanteously or against a single reference. If you are unsure which one is the appropriate GenomeMapper, you might want to use the latter https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2768987/

Address of the bookmark: http://1001genomes.org/software/genomemapper.html

BASE: a practical de novo assembler for large genomes using long NGS reads

Rahul Nayak — Fri, 19 Oct 2018 07:25:21 -0500

new de novo assembler called BASE. It enhances the classic seed-extension approach by indexing the reads efficiently to generate adaptive seeds that have high probability to appear uniquely in the genome. Such seeds form the basis for BASE to build extension trees and then to use reverse validation to remove the branches based on read coverage and paired-end information, resulting in high-quality consensus sequences of reads sharing the seeds. Such consensus sequences are then extended to contigs.

Address of the bookmark: https://github.com/dhlbh/BASE

Gepard: allows the calculation of dotplots even for large sequences like chromosomes or bacterial genomes

Jit — Mon, 26 Aug 2019 11:38:30 -0500

Gepard (German: "cheetah", Backronym for "GEnome PAir - Rapid Dotter") allows the calculation of dotplots even for large sequences like chromosomes or bacterial genomes. Reference: Krumsiek J, Arnold R, Rattei T. Gepard: A rapid and sensitive tool for creating dotplots on genome scale. Bioinformatics 2007; 23(8): 1026-8. PMID: 17309896

http://cube.univie.ac.at/gepard

Address of the bookmark: https://github.com/univieCUBE/gepard

Chromonomer: a tool set for repairing and enhancing assembled genomes through integration of genetic maps and conserved synteny

Jit — Mon, 17 Feb 2020 05:38:46 -0600

Chromonomer is a program designed to integrate a genome assembly with a genetic map. Chromonomer tries very hard to identify and remove markers that are out of order in the genetic map, when considered against their local assembly order; and to identify scaffolds that have been incorrectly assembled according to the genetic map, and split those scaffolds.

Address of the bookmark: http://catchenlab.life.illinois.edu/chromonomer/

PyParanoid: a pipeline for rapid identification of homologous gene families in a set of genomes

BioStar — Thu, 13 Aug 2020 10:06:19 -0500

PyParanoid is a pipeline for rapid identification of homologous gene families in a set of genomes - a central task of any comparative genomics analysis. The "gold standard" for identifying homologs is to use reciprocal best hits (RBHs) which depends on performing a all-vs-all sequence comparison, usually using BLAST, to determine homology. However, these methods are computationally expensive, requiring O(n2) resources to identify RBHs. This is problematic, as the modern deluge of sequencing data means that comparative genomics analyses could be performed on datasets of thousands of strains.

Address of the bookmark: https://github.com/ryanmelnyk/PyParanoid

OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes

Abhi — Tue, 02 May 2023 00:48:28 -0500

OrthoVenn3 is a powerful tool for comparative genomics analysis, used as a web server for full genome comparisons, annotation, and evolutionary analysis of orthologous clusters across multiple species. It has already been used by thousands of users from over 60 countries.

Address of the bookmark: https://orthovenn3.bioinfotoolkits.net/

NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes

LEGE — Tue, 10 Sep 2024 04:54:55 -0500

NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes

NGenomeSyn [multiple (N) Genome Synteny], for publication-ready visualization of syntenic relationships of the whole genome or local region and genomic features (e.g. repeats, structural variations, genes) across multiple genomes with a high customization. NGenomeSyn provides an easy way for its users to visualize a large amount of data with a rich layout by simply adjusting options for moving, scaling, and rotation of target genomes. Moreover, NGenomeSyn could be applied on the visualization of relationships on non-genomic data with similar input formats.

https://academic.oup.com/bioinformatics/article/39/3/btad121/7072460

Address of the bookmark: https://github.com/hewm2008/NGenomeSyn

Tigers genome sequenced

Rahul Agarwal — Tue, 17 Sep 2013 16:48:24 -0500

Fifteen scientists led by Dr Jong Bhak of Genome Research Foundation, South Korea, decoded as many as 3 billion nucleotides (organic molecules that form the basic building blocks of nucleic acids, such as DNA). They identified 20,000 genes related to various functions of the tiger.

The biggest and perhaps most fearsome of the world's big cats, the tiger, shares 95.6 percent of its DNA with humans' cute and furry companions, domestic cats.

The new research showed that big cats have genetic mutations that enabled them to be carnivores. The team also identified mutations that allow snow leopards to thrive at high altitudes.

Reference:

http://www.nbcnews.com/science/your-cat-ferocious-tigers-share-lot-95-6-percent-their-4B11182690

http://timesofindia.indiatimes.com/home/environment/flora-fauna/Gene-mapping-of-tiger-completed/articleshow/22671681.cms

Paper:

http://www.nature.com/ncomms/2013/130917/ncomms3433/full/ncomms3433.html