BOL: Related items

chromosight: Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps

Jit — Mon, 23 Mar 2020 06:20:04 -0500

Python package to detect chromatin loops (and other patterns) in Hi-C contact maps.

Stable version with pip:

pip3 install --user chromosight

Stable version with conda:

conda install -c bioconda -c conda-forge chromosight

or, if you want to get the latest development version:

pip3 install --user -e git+https://github.com/koszullab/chromosight.git@master#egg=chromosight

Address of the bookmark: https://github.com/koszullab/Chromosight

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/

Picard

Neel — Fri, 29 Apr 2016 08:21:54 -0500

Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file formats are defined in the Hts-specs repository. See especially the SAM specification and the VCF specification.

Note that the information on this page is targeted at end-users. For developers, the source code, building instructions and implementation/development resources are available on GitHub.

The Picard toolkit is open-source under the MIT license and free for all uses.

Enjoy!

Address of the bookmark: http://broadinstitute.github.io/picard/

Andi

Jit — Fri, 13 May 2016 05:16:35 -0500

This is the andi program for estimating the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because andi does not compute full alignments, it is so efficient that it scales even up to thousands of bacterial genomes.

This readme covers all necessary instructions for the impatient to get andi up and running. For extensive instructions please consult the manual.

More at https://github.com/evolbioinf/andi/

Address of the bookmark: http://bioinformatics.oxfordjournals.org/content/early/2015/01/13/bioinformatics.btu815.full

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/

HivePlot

Jit — Thu, 16 Feb 2017 11:39:34 -0600

The hive plot is a rational visualization method for drawing networks. Nodes are mapped to and positioned on radially distributed linear axes — this mapping is based on network structural properties. Edges are drawn as curved links. Simple and interpretable.

The purpose of the hive plot is to establish a new baseline for visualization of large networks — a method that is both general and tunable and useful as a starting point in visually exploring network structure.

More at http://www.hiveplot.com/

Address of the bookmark: http://www.hiveplot.com/

SVfinder: Tool for detecting genomic rearrangement form DNA-seq data

Robert M Willioms — Thu, 14 Dec 2017 15:51:40 -0600

SVfinder provides genome-wide detection of structural variants from next generation paired-end sequencing reads.

Address of the bookmark: https://github.com/cauyrd/SVfinder

GMOL: An Interactive Tool for 3D Genome Structure Visualization

Jit — Wed, 21 Mar 2018 12:25:20 -0500

GMOL was developed based upon our multi-scale approach that allows a user to scale between six separate levels within the genome. With GMOL, a user can choose any unit at any scale and scale it up or down to visualize its structure and retrieve corresponding genome sequences.

Address of the bookmark: https://www.nature.com/articles/srep20802

G-NEST: The Gene NEighborhood Scoring Tool

Neel — Fri, 25 Sep 2020 20:09:18 -0500

The Gene NEighborhood Scoring Tool (G-NEST) combines genomic location, gene expression, and evolutionary sequence conservation data to score putative gene neighborhoods across all window sizes. Primary author of final code = William F. Martin. Example data files are in the separate repository.

Address of the bookmark: https://github.com/dglemay/G-NEST