BOL: Related items

SVEngine: Allele Specific and Haplotype Aware Structural Variants Simulator

Jit — Sat, 04 Jul 2020 05:52:34 -0500

SVEngine (Structural Variants Engine)

SVEngine is a multi-purpose and self-contained simulator for whole genome scale spike-in of thousands of SV events of various types in both single-sample and matched sample scenarios.
SVEngine takes as input reference contigs in FASTA files, variant meta distribution as specified in META files (see Manual) or specific variant information as specified in VAR files (see Manual) and NEWICK files for specifying clonal phylogenetic trees in cancer.
SVEngine outpus alterred contigs in FASTA files, spiked-in variants in VAR files (see Manual), simulated short read in FASTQ files and aligned short reads in BAM files.

Address of the bookmark: https://bitbucket.org/charade/svengine/src/master/

sim3C: Read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC)

Jit — Tue, 13 Nov 2018 07:25:38 -0600

Required python modules

biopython
intervaltree
numpy
scipy
tqdm
PyYAML

Address of the bookmark: https://github.com/cerebis/sim3C

Easyfig

Poonam Mahapatra — Fri, 29 Apr 2016 05:49:39 -0500

Easyfig has moved to github, for newer releases of Easyfig please visit our new webpage - https://mjsull.github.io/Easyfig. Easyfig is a Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface (GUI).

More at http://easyfig.sourceforge.net/

Address of the bookmark: http://easyfig.sourceforge.net/

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)

GKNO

Neel — Fri, 20 May 2016 18:56:37 -0500

gkno opens the world of complex bioinformatic analysis to people of all level of computational expertise. This site contains documentation, tutorials and information on all the tools that comprise gkno.

http://gkno.me/how-to/install.html

http://gkno.me/software.html

Address of the bookmark: http://gkno.me/

LoRMA: a tool for correcting sequencing errors in long reads such those produced by Pacific Biosciences sequencing machines

Jit — Wed, 15 Jun 2016 17:18:36 -0500

LoRMA is a tool for correcting sequencing errors in long reads such those produced by Pacific Biosciences sequencing machines.

Publication:

L. Salmela, R. Walve, E. Rivals, and E. Ukkonen: Accurate selfcorrection of errors in long reads using de Bruijn graphs. Accepted to RECOMB-Seq 2016.

Download:

Address of the bookmark: https://www.cs.helsinki.fi/u/lmsalmel/LoRMA/

EasyBuild

Jit — Fri, 27 Jan 2017 16:00:43 -0600

EasyBuild is a software build and installation framework that allows you to manage (scientific) software on High Performance Computing (HPC) systems in an efficient way.
A full list of supported software packages is available here.

Address of the bookmark: https://hpcugent.github.io/easybuild/

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/

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

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