BOL: Related items

Want to Know which genome assembler rule the world ?

Rahul Agarwal — Sun, 11 Aug 2013 11:42:32 -0500

Assemblathon 2: evaluating de novo methods of genome assembly

http://www.gigasciencejournal.com/content/2/1/10/abstract

http://blogs.nature.com/news/2013/07/genome-assembly-contest-prompts-soul-searching.html

http://assemblathon.org/post/44431915644/feedback-and-analysis-of-the-assemblathon-2-p

Barber pole worm , sheep pathogen sequenced !!!

Rahul Agarwal — Tue, 03 Sep 2013 16:32:18 -0500

Haemonchus contortus is a highly pathogenic parasitic nematode of that can infect a large number of wild and domesticated ruminant species and is the most economically important parasite of sheep and goats worldwide. Scientists at the Wellcome Trust Sanger Institute have sequenced the genome of the barber's pole worm (Haemonchus contortus), which will help to explore the this tropical parasite which been disseminated around the world by livestock movement.

H. contortus is a member of the superfamily trichostrongyloidea (Strongylida) which contains most of the economically important parasitic nematodes of grazing livestock. These parasites cost the global livestock industry billions of dollars per annum in lost production and drug costs. A common type of clover may be a preventative or palliative for the disease. However, some particular breeds of sheep, such as the Gulf Coast Native from the Southern United States, have been shown to have developed special resistance to H. contortus.

Getting the full genome can help to tackle the problem and understand the resistance mechanism with an ease. Moreover, the genome could now provide a comprehensive understanding of how treatments against parasitic worms work and point to further new treatments and vaccines. By comparing the genome of the barber's pole worm with those of worms that have acquired drug resistance, researchers expect to reveal information about how and why resistance has occurred. Till now, researchers have uncovered essential information in the fight against drug resistance in worms.

Reference:

http://www.fwi.co.uk/articles/28/08/2013/140758/researchers-close-in-on-worm-resistance-in-sheep.htm

http://www.sciencedaily.com/releases/2013/08/130828103351.htm?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+sciencedaily%2Fplants_animals+(ScienceDaily%3A+Plants+%26+Animals+News)

Image source: Wikipedia

DNA tale of 3 to 4 years old Serbia boy

Rahul Agarwal — Tue, 26 Nov 2013 17:34:00 -0600

The genome of a young boy found underground at Mal’ta near Lake Baikal of eastern Siberia around 24,000 years ago came out as close relative of Europeans and Native Indians.

Link:

http://www.nytimes.com/2013/11/21/science/two-surprises-in-dna-of-boy-found-buried-in-siberia.html?_r=0

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12736.html

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

How to sequence the human genome - Mark J. Kiel

Fri, 30 May 2014 13:24:11 -0500

View full lesson: http://ed.ted.com/lessons/how-to-sequence-the-human-genome-mark-j-kiel Your genome, every human's genome, consists of a unique DNA sequence of A's, T's, C's and G's that tell your cells how to operate. Thanks to technological advances, scientists are now able to know the sequence of letters that makes up an individual genome relatively quickly and inexpensively. Mark J. Kiel takes an in-depth look at the science behind the sequence. Lesson by Mark J. Kiel, animation by Marc Christoforidis.

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/

Grinder / Biogrinder - A versatile omics shotgun and amplicon sequencing read simulator

Jit — Wed, 24 May 2017 08:41:41 -0500

Grinder is a versatile program to create random shotgun and amplicon sequence libraries based on DNA, RNA or proteic reference sequences provided in a FASTA file.

Grinder can produce genomic, metagenomic, transcriptomic, metatranscriptomic, proteomic, metaproteomic shotgun and amplicon datasets from current sequencing technologies such as Sanger, 454, Illumina. These simulated datasets can be used to test the accuracy of bioinformatic tools under specific hypothesis, e.g. with or without sequencing errors, or with low or high community diversity. Grinder may also be used to help decide between alternative sequencing methods for a sequence-based project, e.g. should the library be paired-end or not, how many reads should be sequenced.

Address of the bookmark: https://sourceforge.net/projects/biogrinder/files/biogrinder/

Jabba: Hybrid Error Correction for Long Sequencing Reads

Jit — Fri, 05 Jan 2018 03:58:14 -0600

Jabba is a hybrid error correction tool to correct third generation (PacBio / ONT) sequencing data, using second generation (Illumina) data.

Input

Jabba takes as input a concatenated de Bruijn graph and a set of sequences:

the de Bruijn graph should appear in fasta format with 1 entry per node, the meta information should be in the format:
>NODE
the set of sequences should be in fasta or fastq format. These sequences will be corrected (e.g. PacBio reads). The corrections will be written to a file Jabba fasta.
The output is a file in fasta format with corrections of the long reads, and additionally a file in the input format containing uncorrected reads.

https://github.com/biointec/jabba/wiki

https://almob.biomedcentral.com/articles/10.1186/s13015-016-0075-7

Address of the bookmark: https://github.com/biointec/jabba

Scientist Bioinformatics Positions

Thu, 30 Jan 2020 06:53:40 -0600

Bioinformatics-Multi_Omics_Integration

https://www.researchgate.net/job/939073_Senior_Scientist_Bioinformatics-Multi_Omics_Integration

Senior_Scientist_Bioinformatics-Transcriptomics_Analysis

https://www.researchgate.net/job/939075_Senior_Scientist_Bioinformatics-Transcriptomics_Analysis-Belgium_France_Switzerland_The_Netherlands

Senior Scientist Bioinformatics - Network Analytics

https://www.researchgate.net/job/939070_Senior_Scientist_Bioinformatics-Network_Analytics_Belgium_France_Switzerland_the_Netherlands

Team Leader Bioinformatics Data Sciences - Mechelen, Belgium

https://www.researchgate.net/job/938787_Team_Leader_Bioinformatics_Data_Sciences-Mechelen_Belgium