BOL: Related items

Qualimap2: Evaluating next generation sequencing alignment data

Jit — Tue, 11 Sep 2018 04:44:29 -0500

Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.

Supported types of experiments include:

Whole-genome sequencing
Whole-exome sequencing
RNA-seq (speical mode available)
ChIP-seq

Address of the bookmark: http://qualimap.bioinfo.cipf.es/

jtools : more efficient presentation of regression analyses

Neel — Tue, 11 Feb 2020 23:10:49 -0600

This package consists of a series of functions created by the author (Jacob) to automate otherwise tedious research tasks. At this juncture, the unifying theme is the more efficient presentation of regression analyses. There are a number of functions for other programming and statistical purposes as well. Support for the survey package’s svyglm objects as well as weighted regressions is a common theme throughout.

Notice: As of jtools version 2.0.0, all functions dealing with interactions (e.g., interact_plot(), sim_slopes(), johnson_neyman()) have been moved to a new package, aptly named interactions.

Address of the bookmark: https://cran.r-project.org/web/packages/jtools/readme/README.html

Circos visualization !

BioStar — Mon, 06 Mar 2023 06:01:32 -0600

Circos visualization

https://wlcb.oit.uci.edu/modules/index.html

Address of the bookmark: https://wlcb.oit.uci.edu/NG-Circos

Recombination detection tool

Jit — Tue, 02 Feb 2016 10:11:14 -0600

A program to detect recombination hotspots using population genetic data.

More at https://github.com/auton1/LDhot

Address of the bookmark: https://github.com/auton1/LDhot

Release Notes for Genome Workbench 2.10.5

Jit — Thu, 12 May 2016 13:49:41 -0500

New Features in latest release

New ProSplign tool integrated with Genome Workbench (Tutorial, Video)
New export function for BAM/cSRA coverage graphs (Tutorial)
New export function for alignments GFF3 format ((Tutorial))
Tree View: implemented new export mode based on selections (tutorial coming)
Tree View: added support for distance based circular trees
Tree View: new rooting mode (Midpoint Root) results in more balanced trees (Tutorial)
Tree View: added possibility to right-click on an edge between two nodes and "Place Root at Middle of Branch" – to re-root at mid-branch (Tutorial)

Bpipe - a tool for running and managing bioinformatics pipelines

Radha Agarkar — Sat, 21 May 2016 22:42:16 -0500

Bpipe provides a platform for running big bioinformatics jobs that consist of a series of processing stages - known as 'pipelines'.

January 20th, 2016 - New! Bpipe 0.9.9 released!
Download latest, all
Documentation
Mailing List (Google Group)

Bpipe has been published in Bioinformatics! If you use Bpipe, please cite:

Sadedin S, Pope B & Oshlack A, Bpipe: A Tool for Running and Managing Bioinformatics Pipelines, Bioinformatics

Address of the bookmark: http://docs.bpipe.org/

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/

maf2synteny

Abhimanyu Singh — Thu, 18 May 2017 05:31:30 -0500

A tool for converting for recovering synteny blocks from multiple alignment (in MAF fromat)

This tool is a standalone version of Ragout module [http://fenderglass.github./Ragout]

Address of the bookmark: https://github.com/fenderglass/maf2synteny

PhyloGrapher - Graph Visualization Tool

Jit — Wed, 07 Mar 2018 18:11:25 -0600

PhyloGrapher is a program designed to visualize and study evolutionary relationships within families of homologous genes or proteins (elements). PhyloGrapher is a drawing tool that generates custom graphs for a given set of elements. In general, it is possible to use PhyloGrapher to visualize any type of relations between elements.

https://www.youtube.com/watch?v=WgufqYMHCvM

Address of the bookmark: http://www.atgc.org/PhyloGrapher/PhyloGrapher_Welcome.html

SynVisio: An Interactive Multiscale Synteny Visualization Tool for McScanX.

Jit — Sun, 31 May 2020 02:01:14 -0500

SynVisio lets you explore the results of McScanX a popular synteny and collinearity detection toolkit and generate publication ready images.

SynVisio requires two files to run:

The simplified gff file that was used as an input for a McScanX query.
The collinearity file generated as an output by McScanX for the same input query.
Optional track file in bedgraph format to annotate the generated charts.

SynVisio offers different types of visualizations such as Linear Parallel plots, Hive plots, Stacked Parallel Plots and Dot plots. Users can configure the type of plots required and then choose the source and the target chromosomes that need to be mapped. Users also have option to download the generated visualizations in publication ready SVG or PNG formats.

Address of the bookmark: https://synvisio.github.io/#/