BOL: Related items

JSON

Abhimanyu Singh — Tue, 04 Apr 2017 08:02:39 -0500

JSON (JavaScript Object Notation) is a lightweight data-interchange format. It is easy for humans to read and write. It is easy for machines to parse and generate. It is based on a subset of the JavaScript Programming Language, Standard ECMA-262 3rd Edition - December 1999. JSON is a text format that is completely language independent but uses conventions that are familiar to programmers of the C-family of languages, including C, C++, C#, Java, JavaScript, Perl, Python, and many others. These properties make JSON an ideal data-interchange language.

JSON is built on two structures:

A collection of name/value pairs. In various languages, this is realized as an object, record, struct, dictionary, hash table, keyed list, or associative array.
An ordered list of values. In most languages, this is realized as an array, vector, list, or sequence.

These are universal data structures. Virtually all modern programming languages support them in one form or another. It makes sense that a data format that is interchangeable with programming languages also be based on these structures.

Address of the bookmark: http://json.org/

Pandoc: a universal document converter

Surabhi Chaudhary — Thu, 24 Jun 2021 01:33:47 -0500

If you need to convert files from one markup format into another, pandoc is your swiss-army knife. Pandoc can convert almost all formats

https://pandoc.org/index.html

Address of the bookmark: https://pandoc.org/

MafTools

Jit — Thu, 16 Feb 2017 11:16:01 -0600

maftools - An R package to summarize, analyze and visualize MAF files. Introduction.

With advances in Cancer Genomics, Mutation Annotation Format (MAF) is being widley accepted and used to store variants detected. The Cancer Genome Atlas Project has seqenced over 30 different cancers with sample size of each cancer type being over 200. The resulting data consisting of genetic variants is stored in the form of Mutation Annotation Format. This package attempts to summarize, analyze, annotate and visualize MAF files in an efficient manner either from TCGA sources or any in-house studies as long as the data is in MAF format. Maftools can also handle ICGC Simple Somatic Mutation format.

maftools is on bioRxiv

Please cite the below if you find this tool useful for you.

Mayakonda, A. and H.P. Koeffler, Maftools: Efficient analysis, visualization and summarization of MAF files from large-scale cohort based cancer studies. bioRxiv, 2016. doi: http://dx.doi.org/10.1101/052662

Address of the bookmark: https://github.com/PoisonAlien/maftools

Sequence Tube Maps: displays multiple genomic sequences in the form of a tube map

Jit — Wed, 11 Mar 2020 01:12:06 -0500

A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with vg. (https://github.com/vgteam/vg)

Link to working demo: https://vgteam.github.io/sequenceTubeMap/

Address of the bookmark: https://github.com/vgteam/sequenceTubeMap

Spines

Jitendra Narayan — Tue, 09 Feb 2016 05:07:15 -0600

Spines

Spines is a collection of software tools, developed and used by the Vertebrate Genome Biology Group at the Broad Institute. It provides basic data structures for efficient data manipulation (mostly genomic sequences, alignments, variation etc.), as well as specialized tool sets for various analyses. It also features three sequence alignment packages: Satsuma, a highly parallelized program for high-sensitivity, genome-wide synteny; Papaya, an all-purpose alignment tool for less diverged sequences; and SLAP, a context-sensitive local aligner for diverged sequences with large gaps.

Access Spines here.

http://www.broadinstitute.org/science/programs/genome-biology/spines

Address of the bookmark: http://www.broadinstitute.org/science/programs/genome-biology/spines

Gene Synteny Database

Jit — Fri, 16 Dec 2016 11:09:39 -0600

Comparative genomics remains a pivotal strategy to study the evolution of gene organization, and this primacy is reinforced by the growing number of full genome sequences available in public repositories. Despite this growth, bioinformatic tools available to visualize and compare genomes and to infer evolutionary events remain restricted to two or three genomes at a time, thus limiting the breadth and the nature of the question that can be investigated. Here we present Genomicus, a new synteny browser that can represent and compare unlimited numbers of genomes in a broad phylogenetic view. In addition, Genomicus includes reconstructed ancestral gene organization, thus greatly facilitating the interpretation of the data.

Availability: Genomicus is freely available for online use at http://www.dyogen.ens.fr/genomicus while data can be downloaded at ftp://ftp.biologie.ens.fr/pub/dyogen/genomicus

Contact: rf.sne.eigoloib@crh

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2853686/

DESCHRAMBLER

Jit — Thu, 29 Jun 2017 11:54:59 -0500

DESCHRAMBLER is shown to produce highly accurate reconstructions using data simulation and by benchmarking it against other reconstruction tools

You can find the detail of reconstructed data at http://bioinfo.konkuk.ac.kr/DESCHRAMBLER/

Address of the bookmark: https://github.com/jkimlab/DESCHRAMBLER

chromatiblock: Scalable, whole-genome visualisation of structural changes in prokaryotes

BioStar — Sat, 22 Aug 2020 05:17:18 -0500

To create a fresh environment for chromatiblock to run in do:

conda create --name chromatiblock
conda activate chromatiblock
conda install chromatiblock --channel conda-forge --channel bioconda

Then in future to run chromatiblock you can reactivate this environemtn using conda activate chromatiblock

Direct download:

Alternatively you can download and run the script from here.

Address of the bookmark: https://github.com/mjsull/chromatiblock

JBrowse 2: a modular genome browser with views of synteny and structural variation

Abhi — Tue, 25 Apr 2023 20:58:52 -0500

igvjs - a create-react-app with igv package from npm installed. the igv.js is instrumented to output "DONE" to the console when finished, and to have an increased fetchSizeLimit (which is otherwise git in CRAM longread tests)
jb2-web - stock instance of jbrowse-web v1.7.5
jb1 - stock instance of jbrowse 1 v1.16.11
jb2 embedded - a create-react-app with @jbrowse/react-linear-genome-view

Address of the bookmark: https://github.com/GMOD/jb2profile

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