BOL: Related items

Ktrim: an extra-fast and accurate adapter- and quality-trimmer for sequencing data

Jit — Thu, 11 Feb 2021 21:39:05 -0600

Ktrim is written in C++ for GNU Linux/Unix platforms. After uncompressing the source package, you can find an executable file ktrim under bin/ directory compiled using g++ v4.8.5 and linked with libz v1.2.7 for Linux x86_64 system. If you could not run it (which is usually caused by low version of libc++ or libz library) or you want to build a version optimized for your system, you can re-compile the programs:

user@linux$ make clean && make

Address of the bookmark: https://github.com/hellosunking/Ktrim

Sequencing Solutions to World Health

Rahul Agarwal — Thu, 29 Aug 2013 15:05:35 -0500

"New technology that quickly, easily and economically reveals the genomes of viruses and pathogens transforms public health and medicine."

Source: Life technologies

Address of the bookmark: http://www.lifetechnologies.com/global/en/home/communities-social/blog/blogs/sequencing-solutions-to-world-health.html?cid=social_blogseries_20130829_11098264

Genome Browsers

Rahul Agarwal — Fri, 16 Aug 2013 19:04:47 -0500

Genome Browser is the platform/database used for searching and retreiving sequences and annotation of genomes belong to various eukaryotes, prokaryotes, etc.

Following are the weblink for different available browsers:

http://www.ensembl.org/index.html

http://ensemblgenomes.org/

http://genome.ucsc.edu/

http://www.ncbi.nlm.nih.gov/genome

http://www.ebi.ac.uk/genomes/

http://flybase.org/

http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi

http://www.sanger.ac.uk/resources/databases/

Two major breakthrough!!

Rahul Agarwal — Mon, 02 Sep 2013 10:18:11 -0500

"Scientists in Uruguay in colloboration with European partners sequenced the genome of the high-value Tannat grape, from which "the most healthy of red wines" are fermented.

A quick, $1 syphilis test in development by researchers from UNU-BIOLAC."

Source:

http://www.sciencedaily.com/releases/2013/09/130902101846.htm

http://www.eurekalert.org/pub_releases/2013-09/tca-ssg082613.php

Encode sequencing data freely available to download and use for academic means

Rahul Agarwal — Thu, 13 Mar 2014 18:18:08 -0500

In Encode, regulatory elements investigated via DNA hypersensitivity assays, assays of DNA methylation, and chromatin immunoprecipitation (ChIP) of proteins that interact with DNA, including modified histones and transcription factors, followed by sequencing (ChIP-Seq).

More information:

https://genome.ucsc.edu/ENCODE/pilot.html

Address of the bookmark: https://genome.ucsc.edu/ENCODE/

Tsetse Fly Genome sequenced

Rahul Agarwal — Fri, 25 Apr 2014 10:48:35 -0500

As it reported online today in Science, the team used several sequencing approaches to tackle the tsetse fly's 366 million base genome.

The current study, and companion articles slated to appear in PLOS One, PLOS Genetics, and PLOS Neglected Tropic Diseases, are the result of nearly 150 researchers based in 18 countries.

Source:

http://www.genomeweb.com/sequencing/international-team-sequences-tsetse-fly-genome

GenXPro GmbH

Rahul Agarwal — Thu, 22 May 2014 07:18:35 -0500

GenXPro GMbH is service provider for entire spectrum of nucleotide-based information of any biological sample. By combining intelligent data reduction techniques and latest next generation sequencing technologies, our service portfolio provides most accurate and cost efficient solutions for transcriptomic-, genomic- or epigenomic research.

GENXPRO GMBH, ALTENHÖFERALLEE 3, 60438 FRANKFURT MAIN, GERMANY

Website: http://www.genxpro.info/products_and_services/

PHONE: +49 (0)69- 95 73 97 10, FAX: +49 (0)69- 95 73 97 06

EMAIL: info@genxpro.de

The Genome 10K Project

Tue, 29 Jul 2014 09:11:04 -0500

https://genome10k.soe.ucsc.edu The Genome 10K project aims to assemble a genomic zoo—a collection of DNA sequences representing the genomes of 10,000 vertebrate species, approximately one for every vertebrate genus. The trajectory of cost reduction in DNA sequencing suggests that this project will be feasible within a few years. Capturing the genetic diversity of vertebrate species would create an unprecedented resource for the life sciences and for worldwide conservation efforts. The growing Genome 10K Community of Scientists (G10KCOS), made up of leading scientists representing major zoos, museums, research centers, and universities around the world, is dedicated to coordinating efforts in tissue specimen collection that will lay the groundwork for a large-scale sequencing and analysis project.

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads

Rahul Agarwal — Mon, 06 Jul 2015 08:46:53 -0500

GraphMap is a novel mapper targeted at aligning long, error-prone third-generation sequencing data.
It is designed to handle Oxford Nanopore MinION 1d and 2d reads with very high sensitivity and accuracy, and also presents a significant improvement over the state-of-the-art for PacBio read mappers.

GraphMap was also designed for ease-of-use: the default parameters can handle a wide range of read lengths and error profiles, including: Illumina, PacBio and Oxford Nanopore.
This is an especially important feature for technologies where the error rates and error profiles can vary widely across, or even within, sequencing runs.

http://biorxiv.org/content/early/2015/06/10/020719

Address of the bookmark: https://github.com/isovic/graphmap

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/