BOL: Related items

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

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/#/

Panacus : A Counting Tool for Pangenome Graphs

Neel — Fri, 14 Jun 2024 14:42:28 -0500

panacus is a tool for calculating statistics for GFA files. It supports GFA files with P and W lines, but requires that the graph is blunt, i.e., nodes do not overlap and consequently, each link (L) points from the end of one segment (S) to the start of another.

panacus supports the following calculations:

coverage histogram
pangenome growth statistics
path-/group-resolved coverage table

Address of the bookmark: https://github.com/marschall-lab/panacus

DAVI: Deep learning-based tool for alignment and single nucleotide variant identification

Jit — Tue, 16 Mar 2021 05:41:33 -0500

DAVI consists of models for both global and local alignment and for variant calling. We have evaluated the performance of DAVI against existing state-of-the-art tool sets and found that its accuracy and performance is comparable to existing tools used for bench-marking. We further demonstrate that while existing tools are based on data generated from a specific sequencing technology, the models proposed in DAVI are generic and can be used across different NGS technologies as well as across different species

https://iopscience.iop.org/article/10.1088/2632-2153/ab7e19/pdf

Address of the bookmark: https://github.com/gguptaiitd/NEAT

Circleator

Jit — Sun, 25 Jun 2017 18:04:32 -0500

The Charm City Circleator--or Circleator for short--is a Perl-based visualization tool developed at the Institute for Genome Sciences in the University of Maryland's School of Medicine. Circleator produces circular plots of genome-associated data, like this one:

Common uses of the tool include:

Displaying the sequence and/or genes in a GenBank flat file.
Highlighting differences and/or similarities in gene content between related organisms.
Comparing SNPs and indels between closely-related strains or serovars.
Comparing gene expression values across multiple samples or timepoints.
Visualizing coverage plots of RNA-Seq read alignments.

Key Features

Circleator...

Builds on BioPerl and the input file formats that it supports, including:
- GenBank flat files, GFF, FASTA
Accepts a number of other commonly-used datatypes and file formats:
- BSR and TRF output, SAM/BAM files, VCF-encoded SNPs, tab-delimited files
Outputs publication-ready figures in the SVG (Scalable Vector Graphics) format.
Requires only a single configuration file whose layout mirrors that of the figure itself.
- Predefined configuration files and "track" types are supplied for common datasets.
- Advanced features allow limited analyses to be performed as a figure is drawn.
Includes an extensive set of regression tests.
Offers a prototype web-based GUI (under the "Ringmaster" project.)

https://github.com/jonathancrabtree/Circleator

Address of the bookmark: https://github.com/jonathancrabtree/Circleator

CHSMiner: a GUI tool to identify chromosomal homologous segments

Jit — Sat, 18 Nov 2017 16:55:49 -0600

Background

The identification of chromosomal homologous segments (CHS) within and between genomes is essential for comparative genomics. Various processes including insertion/deletion and inversion could cause the degeneration of CHSs.

Results

Here we present a Java software CHSMiner that detects CHSs based on shared gene content alone. It implements fast greedy search algorithm and rigorous statistical validation, and its friendly graphical interface allows interactive visualization of the results. We tested the software on both simulated and biological realistic data and compared its performance with similar existing software and data source.

Conclusion

CHSMiner is characterized by its integrated workflow, fast speed and convenient usage. It will be useful for both experimentalists and bioinformaticians interested in the structure and evolution of genomes.

https://github.com/zhenwang100/CHSMiner

Address of the bookmark: https://almob.biomedcentral.com/articles/10.1186/1748-7188-4-2

jobTree based python wrapper to run the genome simulation tool suite Evolver

Jit — Fri, 08 Dec 2017 16:26:32 -0600

evolverSimControl (eSC) can be used to simulate multi-chromosome genome evolution on an arbitrary phylogeny (Newick format). In addition to simply running evolver, eSC also automatically creates statistical summaries of the simulation as it runs including text and image files. Also included are convenience scripts to: check on a running simulation and see detailed status and logging information; extract fasta sequence files from the leaf nodes of a completed simulation; extract pairwise multiple alignment files (.maf) from leaf and branch nodes from a completed simulation and with the help of mafJoin, join them together into a single maf covering the entire simulation.

Address of the bookmark: https://github.com/dentearl/evolverSimControl

GPOPSIM: a simulation tool for whole-genome genetic data

Jit — Wed, 17 Jan 2018 03:47:46 -0600

GPOPSIM is a simulation tool for pedigree, phenotypes, and genomic data, with a variety of population and genome structures and trait genetic architectures. It provides flexible parameter settings for a wide discipline of users, especially can simulate multiple genetically correlated traits with desired genetic parameters and underlying genetic architectures.

Address of the bookmark: https://github.com/SCAU-AnimalGenetics/GPOPSIM

%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/