BOL: Related items

MMseqs2.0: ultra fast and sensitive protein search and clustering suite

Jit — Thu, 22 Mar 2018 10:40:51 -0500

MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed.

The MMseqs2 user guide is available as Github Wiki or as PDF file (Thanks to pandoc!)

Please cite: Steinegger M and Soeding J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nature Biotechnology, doi: 10.1038/nbt.3988 (2017).

Address of the bookmark: https://github.com/soedinglab/MMseqs2

MMseqs2: ultra fast and sensitive sequence search and clustering suite

Manisha Mishra — Mon, 18 Jan 2021 10:47:56 -0600

MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed.

Address of the bookmark: https://github.com/soedinglab/MMseqs2

CovCal: Coverage / Read Count Calculator

Jit — Wed, 15 Jun 2016 18:08:13 -0500

Coverage / Read Count Calculator

Calculate how much sequencing you need to hit a target depth of coverage (or vice versa).

Instructions: set the read length/configuration and genome size, then select what you want to calculate.

Written by Stephen Turner, based on the Lander-Waterman formula, inspired by a similar calculator written by James Hadfield. Coverage is calculated as C=LN/G and reads as N=CG/L where C = Coverage (X),L = Read length (bp), G = Haploid genome size (bp), and N = Number of reads. Source code on GitHub.

Address of the bookmark: http://apps.bioconnector.virginia.edu/covcalc/

SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology

Abhimanyu Singh — Tue, 23 May 2017 05:28:56 -0500

SIMBA, SImple Manager for Bacterial Assemblies, is a Web interface for managing assembly projects of bacterial genomes. SIMBA was created to assist bioinformaticians to assemble bacterial genomes sequenced with NextGeneration Sequencing (NGS) platforms quickly, easily and effectively. SIMBA also is open source tool, i.e., can be freely downloaded, shared and modified.

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1344-7

Address of the bookmark: http://ufmg-simba.sourceforge.net/

vt: a variant tool set that discovers short variants from Next Generation Sequencing data.

Jit — Tue, 28 Jan 2020 03:44:43 -0600

vt is a variant tool set that discovers short variants from Next Generation Sequencing data.

https://genome.sph.umich.edu/wiki/Vt

https://github.com/atks/vt

Address of the bookmark: https://genome.sph.umich.edu/wiki/Vt

%MinMax: A versatile tool for calculating and comparing synonymous codon usage and its impact on protein folding.

Surabhi Chaudhary — Thu, 24 May 2018 02:53:31 -0500

%MM calculates whether a given gene sequence encodes amino acids using the most common codons possible, the least common codons possible, or (most typically) some combination of these extremes. See our PLoS ONE paper for more details on how the %MinMax algorithm works. %MinMax results are averaged over an 18-codon sliding window; hence the result for "codon window = 1" is the average codon usage for codons 1-18, codon window 2 = codons 2-19, etc.

Address of the bookmark: http://www.codons.org/

D-GENIES: A tool for Dotplot large Genomes in an Interactive, Efficient and Simple way

Jit — Mon, 11 Jun 2018 09:41:22 -0500

D-GENIES – for Dotplot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualisation. We use minimap version 2 to align the two genomes. Then, the PAF file is parsed and plotted into an interactive plot written with d3.js library. D-Genies also allows to display dot plots from other aligners by uploading their PAF or MAF alignment file. http://dgenies.toulouse.inra.fr/

Address of the bookmark: http://dgenies.toulouse.inra.fr/

Epiviz: an interactive visualization tool for functional genomics data.

Jit — Mon, 09 Jul 2018 05:27:39 -0500

Epiviz is an interactive visualization tool for functional genomics data. It supports genome navigation like other genome browsers, but allows multiple visualizations of data within genomic regions using scatterplots, heatmaps and other user-supplied visualizations. It also includes data from the Gene Expression Barcode project for transcriptome visualization. It has a flexible plugin framework so users can addd3 visualizations. You can see a video tour here.

https://bioconductor.org/packages/release/bioc/html/epivizr.html

https://github.com/epiviz

https://github.com/epiviz/epiviz

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

LRCstats: a tool for evaluating long reads correction methods

Aaryan Lokwani — Wed, 22 Aug 2018 11:05:04 -0500

LRCstats is an open-source pipeline for benchmarking DNA long read correction algorithms for long reads outputted by third generation sequencing technology such as machines produced by Pacific Biosciences. The reads produced by third generation sequencing technology, as the name suggests, are longer in length than reads produced by next generation sequencing technologies, such as those produced by Illumina. However, long reads are plagued by high error rates, which can cause issues in downstream analysis. Long read correction algorithms reduce the error rate of long reads either through self-correcting methods or using accurate, short reads outputted by next generation sequencing technologies to correct long reads.

Address of the bookmark: https://github.com/cchauve/lrcstats

Heatmapper: web-enabled heat mapping for all

Jit — Mon, 01 Oct 2018 08:34:41 -0500

Heatmapper is a freely available web server that allows users to interactively visualize their data in the form of heat maps through an easy-to-use graphical interface. Heatmapper is a versatile tool that allows users to easily create a wide variety of heat maps for many different data types and applications. Heatmapper allows users to generate, cluster and visualize:

1) expression-based heat maps from transcriptomic, proteomic and metabolomic experiments; 2) pairwise distance maps;

3) correlation maps;

4) image overlay heat maps;

5) latitude and longitude heat maps and

6) geopolitical (choropleth) heat maps.

Heatmapper offers a number of simple and intuitive customization options for easy adjustments to each heat map’s appearance and plotting parameters. Heatmapper also allows users to interactively explore their numeric data values by hovering their cursor over each heat map, or by using a searchable/sortable data table view.

Ref https://www.ncbi.nlm.nih.gov/pubmed/27190236

Address of the bookmark: http://www2.heatmapper.ca/