BOL: Related items

GAM-NGS: genomic assemblies merger for next generation sequencing

Jit — Fri, 19 May 2017 07:44:14 -0500

GAM-NGS is a tool able to merge two or more assemblies in order to improve contiguity and correctness. It can be used on all NGS-based assembly projects and it shows its full potential with multi-library Illumina-based projects. With more than 20 available assemblers it is hard to select the best tool. In this context we propose a tool that improves assemblies (and, as a by-product, perhaps even assemblers) by merging them and selecting the generating that is most likely to be correct.

Address of the bookmark: https://github.com/vice87/gam-ngs

Genomic Open-source Breeding informatics initiative

BioStar — Wed, 06 Jan 2021 19:42:21 -0600

To build open-source genomic data management and analysis tools to enable breeders to implement genomic and marker-assisted selection as part of their routine breeding programs.

To transform breeding by connecting diverse data with precision breeding tools to advance yields and adaptation to local growing conditions, bringing global communities closer to a sustainable, reliable food supply.

Address of the bookmark: http://cbsugobii05.biohpc.cornell.edu/wordpress/

BEDOPS v2.4.26: high-performance genomic feature operations

Jit — Mon, 12 Jun 2017 10:11:01 -0500

BEDOPS v2.4.26 is a suite of tools to address common questions raised in genomic studies — mostly with regard to overlap and proximity relationships between data sets. It aims to be scalable and flexible, facilitating the efficient and accurate analysis and management of large-scale genomic data.

The overview section of the BEDOPS v2.4.26 documentation summarizes the toolkit, functionality and performance enhancements. The reference table offers documentation for all applications and scripts.

Address of the bookmark: https://github.com/bedops/bedops

kraken: A universal genomic coordinate translator for comparative genomics

Jit — Thu, 07 Dec 2017 04:45:43 -0600

If you planning on conducting a study involving dozens of large genomes, then you do not have to run all pairwise synteny alignments .. simply try kraken: A universal genomic coordinate translator for comparative genomics

Address of the bookmark: https://github.com/nedaz/kraken

TACOA: Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach

Poonam Mahapatra — Tue, 15 May 2018 09:52:28 -0500

TACOA is a software that can accurately predict the taxonomic origin of genomic fragments from metagenomic data sets by combining the advantages of the k -NN approach with a smoothing kernel function. TACOA can be easily installed and run on a desktop computer, therefore allowing researchers to locally analyze their metagenomic sequence data or integrate it into their pipelines.

Address of the bookmark: http://www.cebitec.uni-bielefeld.de/index.php/2-uncategorised/99-tacoa

sourmash: Quickly search, compare, and analyze genomic and metagenomic data sets.

BioStar — Sat, 06 Jul 2024 04:24:06 -0500

sourmash is a k-mer analysis multitool, and we aim to provide stable, robust programmatic and command-line APIs for a variety of sequence comparisons. Some of our special sauce includes:

FracMinHash sketching, which enables accurate comparisons (including ANI) between data sets of different sizes
sourmash gather, a combinatorial k-mer approach for more accurate metagenomic profiling

Please see the sourmash publications for details.

The name is a riff off of Mash, combined with @ctb's love of whiskey. (Sour mash is used in making whiskey.)

Maintainers: C. Titus Brown (@ctb), Luiz C. Irber, Jr (@luizirber), and N. Tessa Pierce-Ward (@bluegenes).

sourmash was initially developed by the Lab for Data-Intensive Biology at the UC Davis School of Veterinary Medicine, and now includes contributions from the global research and developer community.

Address of the bookmark: https://github.com/sourmash-bio/sourmash

dna2bit: an ultra-fast and accurate genomic distance estimation software

LEGE — Sun, 31 Aug 2025 06:24:58 -0500

dna2bit is a software tool developed in C++11, leveraging the capabilities of OpenMP for parallel computing and the popcount technique for efficient bit manipulation. It has been thoroughly tested using the g++ and clang compilers on both Linux and MacOS platforms.

Address of the bookmark: https://github.com/lijuzeng/dna2bit

irishgrid: Irish Grid Mapping System

Jit — Fri, 26 Dec 2014 07:53:24 -0600

Perl module for creating geographic 10km-square maps using either SVG or PNG (with GD library) output format.

Originally design to map the location of objects in a 10 km map IrishGrid includes:

native support of the Irish Grid System (see http://www.osi.ie/)
optimize for speed (there's as less as possible data to conversion)
customized color functions

https://code.google.com/p/irishgrid/downloads/detail?name=irishgrid.pl

Address of the bookmark: https://code.google.com/p/irishgrid/

Shinyheatmap

Jit — Fri, 21 Oct 2016 05:12:11 -0500

Background: Transcriptomics, metabolomics, metagenomics, and other various next-generation sequencing (-omics) fields are known for their production of large datasets. Visualizing such big data has posed technical challenges in biology, both in terms of available computational resources as well as programming acumen. Since heatmaps are used to depict high-dimensional numerical data as a colored grid of cells, efficiency and speed have often proven to be critical considerations in the process of successfully converting data into graphics. For example, rendering interactive heatmaps from large input datasets (e.g., 100k+ rows) has been computationally infeasible on both desktop computers and web browsers. In addition to memory requirements, programming skills and knowledge have frequently been barriers-to-entry for creating highly customizable heatmaps. Results: We propose shinyheatmap: an advanced user-friendly heatmap software suite capable of efficiently creating highly customizable static and interactive biological heatmaps in a web browser. shinyheatmap is a low memory footprint program, making it particularly well-suited for the interactive visualization of extremely large datasets that cannot typically be computed in-memory due to size restrictions. Conclusions: shinyheatmap is hosted online as a freely available web server with an intuitive graphical user interface: http://shinyheatmap.com. The methods are implemented in R, and are available as part of the shinyheatmap project at: https://github.com/Bohdan-Khomtchouk/shinyheatmap.

More at http://biorxiv.org/content/early/2016/09/21/076463

Address of the bookmark: http://shinyheatmap.com/

Collection of Graph Visualization tools !

Neel — Wed, 25 Jan 2023 02:57:42 -0600

Standard approaches to genome inference and analysis relate sequences to a single linear reference genome. This is efficient but has a fundamental problem: Differences from this reference are hard to observe and describe in a coherent way. Variation and sequence are separated.

https://fungidb.org/fungidb/app/downloads/Current_Release/GultimumBR650/

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