BOL: Related items

Delta: a new Web-based 3D genome visualization and analysis platform

Jit — Wed, 20 Dec 2017 08:49:55 -0600

Delta is an integrative visualization and analysis platform to facilitate visually annotating and exploring the 3D physical architecture of genomes. Delta takes Hi-C or ChIA-PET contact matrix as input and predicts the topologically associating domains and chromatin loops in the genome. It then generates a physical 3D model which represents the plausible consensus 3D structure of the genome. Deltafeatures a highly interactive visualization tool which enhances the integration of genome topology/physical structure with extensive genome annotation by juxtaposing the 3D model with diverse genomic assay outputs.

https://github.com/zhangzhwlab/delta

Address of the bookmark: https://github.com/zhangzhwlab/delta

MGcV: the microbial genomic context viewer for comparative genome analysis

Jit — Mon, 29 Jan 2018 04:55:46 -0600

MGcV is an interactive web-based visalization tool tailored to facilitate small scale genome analysis. To start using MGcV:

Supply your genes/genomic segments/phylogenetic tree of interest in the input-box by
- selecting the type of identifier and pasting identifiers (one per line)
- or by using the gene ID search tool
- or with the BLAST search tool
Click "Visualize context".

Consult the documentation to learn more about MGcV.

Address of the bookmark: http://mgcv.cmbi.ru.nl/

KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies

Jit — Fri, 06 Jul 2018 03:36:45 -0500

KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts. The following tools are currently available in KAT:

hist: Create an histogram of k-mer occurrences from a sequence file. Adds metadata in output for easy plotting.
gcp: K-mer GC Processor. Creates a matrix of the number of K-mers found given a GC count and a K-mer count.
comp: K-mer comparison tool. Creates a matrix of shared K-mers between two (or three) sequence files or hashes.
sect: SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file.
blob: Given, reads and an assembly, calculates both the read and assembly K-mer coverage along with GC% for each sequence in the assembly.SEquence Coverage estimator Tool.
filter: Filtering tools. Contains tools for filtering k-mer hashes and FastQ/A files:
- kmer: Produces a k-mer hash containing only k-mers within specified coverage and GC tolerances.
- seq: Filters a sequence file based on whether or not the sequences contain k-mers within a provided hash.
plot: Plotting tools. Contains several plotting tools to visualise K-mer and compare distributions. The following plot tools are available:
- density: Creates a density plot from a matrix created with the "comp" tool. Typically this is used to compare two K-mer hashes produced by different NGS reads.
- profile: Creates a K-mer coverage plot for a single sequence. Takes in fasta coverage output coverage from the "sect" tool
- spectra-cn: Creates a stacked histogram using a matrix created with the "comp" tool. Typically this is used to compare a jellyfish hash produced from a read set to a jellyfish hash produced from an assembly. The plot shows the amount of distinct K-mers absent, as well as the copy number variation present within the assembly.
- spectra-hist: Creates a K-mer spectra plot for a set of K-mer histograms produced either by jellyfish-histo or kat-histo.
- spectra-mx: Creates a K-mer spectra plot for a set of K-mer histograms that are derived from selected rows or columns in a matrix produced by the "comp".

In addition, KAT contains a python script for analysing the mathematical distributions present in the K-mer spectra in order to determine how much content is present in each peak.

This README only contains some brief details of how to install and use KAT. For more extensive documentation please visit: https://kat.readthedocs.org/en/latest/

https://academic.oup.com/bioinformatics/article/33/4/574/2664339

Address of the bookmark: https://github.com/TGAC/KAT

Juicebox: Visualization and analysis software for Hi-C data

Jit — Fri, 21 Feb 2020 00:33:38 -0600

Juicebox is visualization software for Hi-C data. This distribution includes the source code for Juicebox, Juicer Tools, and Assembly Tools. Download Juicebox here, or use Juicebox on the web. Detailed documentation is available on the wiki. Instructions below pertain primarily to usage of command line tools and the Juicebox jar files.

Juicebox can now be used to visualize and interactively (re)assemble genomes. Check out the Juicebox Assembly Tools Module website https://aidenlab.org/assembly for more details on how to use Juicebox for assembly.

GUI at https://aidenlab.org/juicebox/

Address of the bookmark: https://github.com/aidenlab/Juicebox

RNA-seq workflow: gene-level exploratory analysis and differential expression

Jit — Sat, 09 Oct 2021 07:59:23 -0500

Here we walk through an end-to-end gene-level RNA-seq differential expression workflow using Bioconductor packages. We will start from the FASTQ files, show how these were quantified to the reference transcripts, and prepare gene-level count datasets for downstream analysis. We will perform exploratory data analysis (EDA) for quality assessment and to explore the relationship between samples, perform differential gene expression analysis, and visually explore the results.

Address of the bookmark: http://master.bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html

Bactopia: a flexible pipeline for complete analysis of bacterial genomes

Abhi — Sat, 08 Jun 2024 16:25:08 -0500

Bactopia is a flexible pipeline for complete analysis of bacterial genomes. The goal of Bactopia is process your data with a broad set of tools, so that you can get to the fun part of analyses quicker!

Bactopia was inspired by Staphopia, a workflow we (Tim Read and myself) released that is targeted towards Staphylococcus aureus genomes. Using what we learned from Staphopia and user feedback, Bactopia was developed from scratch with usability, portability, and speed in mind from the start.

Bactopia uses Nextflow to manage the workflow, allowing for support of many types of environments (e.g. cluster or cloud). Bactopia allows for the usage of many public datasets as well as your own datasets to further enhance the analysis of your sequencing. Bactopia only uses software packages available from Bioconda and Conda-Forge to make installation as simple as possible for all users.

To highlight the use of Bactopia and Bactopia Tools, we performed an analysis of 1,664 public Lactobacillus genomes, focusing on Lactobacillus crispatus, a species that is a common part of the human vaginal microbiome. The results from this analysis are published in mSystems under the title: Bactopia: a flexible pipeline for complete analysis of bacterial genomes

Address of the bookmark: https://bactopia.github.io/latest/

Genetic Test in India

Rahul Agarwal — Sun, 11 Aug 2013 10:54:35 -0500

1.Xcode Life Sciences Pvt. Ltd.
6B, Eldorado,
112, Nungambakkam High Road,
Nungambakkam, Chennai 600034
Tamil Nadu, India

2.Mapmygenome™
Royal Demeure,HUDA Techno Enclave,
Plot No. 12/2, Sector-1 500 081
Madhapur,Hyderabad
AP, India

3. DNA Labs India

http://www.dnalabsindia.com/lab.php

4.MedGenome Labs Pvt Ltd
(Division of SciGenom Labs Pvt Ltd.)
Plot no: 43A,SDF, 3rd floor
A Block,CSEZ, Kakanad, Cochin
Kerala - 682037
Phone: 0484 - 2413399
Fax: 0484 - 2413398
Email: info@medgenome.com

5.Narayana Nethralaya

Narayana Hrudayalaya Campus
Narayana Health City
# 258/A, Bommasandra, Hosur Road,
Bangalore - 560 099 - INDIA.
TEL: +91-80-66660655-0658
FAX: +91-80-66660650
Mobile: 9902 821128 (Emergency Only)
e-mail: info@narayananethralaya.com

6.BioAxis DNA Research Centre Private Limited
13-51,Sri Lakshmi Nagar colony,
Besides Big Bazar, Near Kamineni Hospitals
GSI Post BandalGuda (L B Nagar) Hydeabad-500068
Andhra Pradesh (India).
Phone : +91-40-24034503/+91-9246338983

7.Gene Guiide

8th Floor, Embassy Towers, 7 Bungalows Rd, Versova, Andheri West, Mumbai-61
09167 117799
info@geneguiide.com

See more at: http://www.geneguiide.com

8.INDIAN BIOSCIENCES
Regd. Office:
G-2 (Ground Floor Rear), Kailash Colony, New Delhi - 110048, India.
Phone: +91 (0)11 29236088, Email: info@inbdna.com.

9.SRL Limited

GP-26, MARUTI INDUSTRIAL ESTATE,

UDYOG VIHAR,SECTOR-18,

GURGAON - 122015

Tel: 0124-3001243 / 0124-3001209

SRL Limited
VASANT VIHAR, 8, PALAM MARG,
NEW DELHI - 110057
Tel: 011 - 4229 5333

Website: http://www.srlworld.com
National Customer care number:
Call Toll Free : 1800-222-660/1800-102-8282
E-mail id: customercare@srl.in

10.Tata Memorial Centre,

Advanced Centre for Treatment, Research and Education in Cancer

Kharghar, Navi Mumbai - 410 210, INDIA.

Tel: +91-22-2740 5000

Fax: +91-22-2740 5085

E-mail: mail@actrec.gov.in

320000 viruses in mammals yet to sequenced in future!!!

Rahul Agarwal — Tue, 03 Sep 2013 08:35:30 -0500

With current biological technique improvements, finally it is now possible to look at millions of unknown viruses at genomic level and understand the mechanism. According to available data, close to 70 per cent of emerging viral diseases such as HIV/AIDS, West Nile, Ebola, SARS, and influenza, are zoonoses - infections of animals that cross into humans.

To address the challenges of describing and estimating virodiversity, a team of investigators from Center for Infection and Immunity (CII) and EcoHealth Alliance began in jungles of Bangladesh - home to the flying fox.

Reference:

http://economictimes.indiatimes.com/news/news-by-industry/et-cetera/mammals-harbour-at-least-320000-new-viruses/articleshow/22253268.cms

http://www.bbc.co.uk/news/science-environment-23932400

Tigers genome sequenced

Rahul Agarwal — Tue, 17 Sep 2013 16:48:24 -0500

Fifteen scientists led by Dr Jong Bhak of Genome Research Foundation, South Korea, decoded as many as 3 billion nucleotides (organic molecules that form the basic building blocks of nucleic acids, such as DNA). They identified 20,000 genes related to various functions of the tiger.

The biggest and perhaps most fearsome of the world's big cats, the tiger, shares 95.6 percent of its DNA with humans' cute and furry companions, domestic cats.

The new research showed that big cats have genetic mutations that enabled them to be carnivores. The team also identified mutations that allow snow leopards to thrive at high altitudes.

Reference:

http://www.nbcnews.com/science/your-cat-ferocious-tigers-share-lot-95-6-percent-their-4B11182690

http://timesofindia.indiatimes.com/home/environment/flora-fauna/Gene-mapping-of-tiger-completed/articleshow/22671681.cms

Paper:

http://www.nature.com/ncomms/2013/130917/ncomms3433/full/ncomms3433.html

An entire genome written in lab

Rahul Nayak — Fri, 25 Oct 2013 09:43:03 -0500

This is the first time ever the genetic code has been fundamentally changed. The breakthrough is a huge step forward in synthetic biology and opens up the possibility of turning re-coded bacteria into biofactories, capable of producing potent new forms of protein that could fight disease or generate sustainable materials.

More @ http://news.yale.edu/2013/10/17/researchers-rewrite-entire-genome-and-add-healthy-twist

News Reference: Yale news

Image Source: Sciencedaily.