BOL: Related items

Fastq format

Jit — Wed, 03 May 2017 04:23:32 -0500

FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. Both the sequence letter and quality score are each encoded with a single ASCII character for brevity.

It was originally developed at the Wellcome Trust Sanger Institute to bundle a FASTA sequence and its quality data, but has recently become the de facto standard for storing the output of high-throughput sequencing instruments such as the Illumina Genome Analyzer.^[1]

Address of the bookmark: https://en.wikipedia.org/wiki/FASTQ_format

Quick next generation sequencing (NGS) terms definition

Neel — Fri, 09 Jun 2017 04:52:26 -0500

fragment size: the Illumina WGS protocol generates paired-end reads from both ends of longer fragments. The lengths of these fragments are assumed to be sampled from a normal distribution. Therefore, in the absence of structural variants, mapping locations of the paired ends span within an interval [δmin,δmax]. Most (>90%) of paired-end reads are sampled from no-SV regions, therefore the fragment size distribution can be learned empirically for each WGS data set separately.

concordant reads: a read pair is called concordant if they can be mapped to the reference genome as “expected”: (a) mapped to opposing strands where the upstream read is mapped to the forward strand and the downstream read is mapped to the reverse strand2, (b) the distance between ends is between the minimum and maximum expected fragment size.

discordant reads: briefly, any non-concordant read pair is considered discordant. Note that, by definition, the discordant read pairs signal potential SVs. The sequence signature produced by these type of reads is known as read-pair signature.

split reads: a read that can only be mapped to the reference genome by breaking into two sub-reads is called a split-read. These types of reads also indicate a potential SV or a short insertion or deletion (indel).

read depth: number of reads that map within a region of the genome. Overall genome-wide read depth is also referred to as depth of coverage. It is expected that the number of reads that “cover” each base-pair to follow a Poisson distribution. Therefore, if the read depth over a certain region deviates significantly from this distribution, it signals for a potential copy number variation (CNV).

PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool

Jit — Fri, 01 Dec 2017 04:10:54 -0600

PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms.

Relying on unique software architecture, PLAST takes full advantage of recent multi-core personal computers without requiring any additional hardware devices.

PLAST stands for Parallel Local Sequence Alignment Search Tool and is was published in BMC Bioinformatics.

PLAST is a general purpose sequence comparison tool providing the following benefits:

PLAST is a high-performance sequence comparison tool designed to compare two sets of sequences (query vs. reference),
Reduces the processing time of sequences comparisons while providing highest quality results,
Contains a fully integrated data filtering engine capable of selecting relevant hits with user-defined criteria (E-Value, identity, coverage, alignment length, etc.),
Does not require any additional hardware, since it is a software solution. It is easy to install, cost-effective, takes full advantage of multi-core processors and uses a small RAM footprint,
Ready to be used on desktop computer, cluster, cloud as well as within distributed system running Hadoop.

https://plast.inria.fr/

Address of the bookmark: https://plast.inria.fr/

Convert EnsEMBL GTF to Annotation table (Geneid, GeneSymbol, GeneWiseChrLocation, GeneClass, Strand) Raw

EagleEye — Fri, 24 Jun 2016 18:08:49 -0500

Bash Script source:

https://gist.github.com/santhilalsubhash/367befcf5216be4b1fd9

Information:

This script converts EnsEMBL GTF (Ex: https://gist.githubusercontent.com/santhilalsubhash/1e7cca357e52a181dc25/raw/cfb803e07900a2baefbb6534f1299fd30cb57a29/sample.GTF) file to annotation table format. It generated two files
1) Transcript wise chromosome location with information about transcripts (Ex: https://gist.githubusercontent.com/santhilalsubhash/c7dec516e0338503a4b6/raw/de0af1a39f0005c4ce7321c5ae57fc8b4a14c7f4/sample.GTF_enst_annotation.txt)
2) Gene wise chromosome location with information about genes (Ex: https://gist.githubusercontent.com/santhilalsubhash/c92006c5080f0333bec2/raw/d16e0b2440d73b09b486d3c9751cdb248a73fa0b/sample.GTF_ensg_annotation.txt)

Note: You can download GTF files from http://www.ensembl.org/info/data/ftp/index.html

nQuire: a statistical framework for ploidy estimation using next generation sequencing

Jit — Thu, 04 Oct 2018 05:23:59 -0500

nQuire provides a statistical framework to study organisms with intraspecific variation in ploidy. nQuire is likely to be useful in epidemiological studies of pathogens, artificial selection experiments, and for historical or ancient samples where intact nuclei are not preserved. It is implemented as a stand-alone Linux command line tool in the C programming language and is available at https://github.com/clwgg/nQuireunder the MIT license.

Address of the bookmark: https://github.com/clwgg/nQuireunder

Research opening @ IBAB, Bengaluru

Mon, 28 Jan 2019 17:45:54 -0600

Applications are invited for the position of Project Assistant in Bio-IT centre at IBAB, Electronic city, Bengaluru. The successful candidate will work in the next-generation sequencing (NGS) facility to perform nucleic acid isolations, quality and quantity analyses, NGS library preparations, and maintenance of sequencing related instruments and other related lab equipment. In addition, the candidate is expected to assist in various administrative matters including procurement, maintaining inventory of laboratory consumables etc. The person will have opportunity to get expertise in entire pipeline of NGS. After sufficient training, the person will act as a demonstrator in the workshops conducted by Bio-IT centre.
Essential Qualifications, Experiences, and Skills:

1. MSc. or B. Tech. or equivalent degree in Biotechnology or related life sciences discipline.
2. Strong aptitude for laboratory work and should be detail-oriented person.
3. Hands-on experience in basic molecular biology techniques.
4. Prior experience in working in a research laboratory or industry.
5. Basic IT skills that include familiarity with Microsoft Office packages.
6. Ability to carry out basic maintenance of general lab equipments and laboratory resources.
7. Ability to maintain accurate records of laboratory work.
8. Willingness to learn, and should be a team player.
Desirable Experience and Skills:
1. Familiarity with NGS technology.
2. Experience in preparation of NGS libraries.
3. Familiarity with Sanger sequencing technology (capillary electrophoresis based)

Remuneration: Remuneration will commensurate with expertise and experience.

How to Apply: Interested applicants fulfilling the criteria may send their detailed CV and a cover letter that explains their suitability for this position, in a single PDF, to Dr. Sreekanth Reddy at careers_bioit@ibab.ac.in. Last date for submission of application is 23rd February 2019. Please mention the position applying for in the subject line of the email.

About IBAB: The Bio-IT Centre at IBAB has state-of-art sequencing facility with the HiSeq 2500 and accessories such as Qubit, Covaris, Agilent 2200 TapeStation, Stratagene Mx 3000 for next generation sequencing, 3500 Dx Genetic Analyzer for capillary electrophoresis based sequencing, and HiScan for microarray imaging. The facility is fully operational and providing services to the scientific community. The Institute of Bioinformatics and Applied Biotechnology (IBAB) is a unique institute engaged in education, research and entrepreneur support programs and is based at Electronic City, Bangalore. IBAB’s mission is to catalyze the growth of the biotechnology and bioinformatics industries in India. To know more please visit: http://www.ibab.ac.in/index.php/bioit/

Simka and SimkaMin are comparative metagenomics method dedicated to NGS datasets

Neel — Sat, 06 Jul 2019 13:56:10 -0500

Simka is a de novo comparative metagenomics tool. Simka represents each dataset as a k-mer spectrum and compute several classical ecological distances between them.

Developper: Gaëtan Benoit, PhD, former member of the Genscale team at Inria.

Contact: claire dot lemaitre at inria dot fr

Simka and SimkaMin are comparative metagenomics method dedicated to NGS datasets. https://gatb.inria.fr/software/simka/

Address of the bookmark: https://github.com/GATB/simka

Industrial Training in Computer Aided Drug Designing (CADD)

RASA Life Sciences — Wed, 13 Nov 2019 05:00:44 -0600

Learn More about Computer Aided Drug Designing (CADD)!!!

#rasalsi #rasa In our Industrial program you will get Knowledge on RNA Seq, CHIP Seq,

Batch Starts From 18^th November 2019

#hurryup #registernow #enquirenow The primary goal of the industrial training program is to provide students with necessary skills making with employable. RASA LSI trains students with the enhanced skills required for them to excel in jobs in biotechnology, pharmaceuticals, BioIT and related industry sectors. At Rasa you will learn from industry leaders how to apply these skills in life science & have a command over software developing process by using various methodologies. For Registration visit us on: https://www.rasalsi.com/index.php/front-page/industrial-training/

Post Doc Computational Biology, Bioinformatics - Network Biology & Data Science, NGS (m/f/d)

Sat, 15 Feb 2020 06:13:35 -0600

https://www.jobvector.de/jobs-stellenangebote/biologie-life-sciences/forschung-entwicklung/post-doc-computational-biology-bioinformatics-network-biology-data-science-ngs-129867.html?suid=e522e9793b41817e52ac58d6963b94e2519920df

Requirements
Doctoral degree in Bioinformatics, Computational Biology, (Bio)physics/-mathematics, Biochemistry/Biology or similar with strong quantitative and numeric focus
Ability to numerically process complex and large data sets
Good programming skills (R/Bioconductor and/or Python preferred, Linux is a plus)
Experience in analyzing next-generation sequencing data sets using network biology
Scientific publication record in applied bioinformatics
Familiarity with single cell NGS analyses and other –omics techniques is a plus, but not essential

10 NGS services companies around the globe !

BioStar — Sun, 22 Nov 2020 23:56:17 -0600

The global NGS services market is expected to reach USD 13.1 billion by 2025. Here are the top 10 NGS services companies to look for –

1. Illumina, Inc. (U.S.)

Illumina, Inc. was founded in 1998 and is headquartered at San Diego, U.S. Illumina, Inc. is one of the leading players in DNA sequencing and array-based technologies, serving customers in the research, clinical, and applied markets. The company offers products for applications in the life sciences, oncology, reproductive health, agriculture, and other emerging segments. The company serves government laboratories, genomic research centers, academics institutions as well as pharmaceutical, biotechnology, agrigenomics, commercial molecular diagnostics laboratories and consumer genomics companies. Illumina, Inc. has its geographic presence in North America, Europe, Latin America, Asia-pacific, and others.

2. QIAGEN N.V. (Netherlands)

QIAGEN N.V. was incorporated in 1986 and is headquartered at Venlo, The Netherlands. The Company is engaged in providing Sample to Insight solutions that transform biological samples into molecular insights. QIAGEN provides its workflow to customers in molecular diagnostics, assay technologies, bioservices and automation systems. The company’s genome services are suitable for custom/tailored projects that allow access to genomic sequence information. The Company market its products in more than 100 countries across the Americas, Europe, Asia, Australia, and the Middle-East &Africa through its subsidiaries and channel partners.

3. PerkinElmer, Inc. (U.S.)

PerkinElmer, Inc. was founded in 1947 and is headquartered in Waltham, Massachusetts, the U.S. PerkinElmer, Inc. offers its products & services and solutions for the diagnostics, food, environmental, industrial, life sciences research and laboratory services markets. The company offer comprehensive genetic testing solutions that help to provide insight into the complex nature of rare and inherited diseases. Some of the subsidiaries of the company are Caliper Life Sciences, Improvision, Viacell Inc., ViaCord LLC, among many others. The company has its facilities located in Europe (France, Germany, and Belgium), U.S. and Asia (China, India, and Japan).

4. Eurofins Scientific SE (Luxembourg)

Eurofins Scientific SE was founded in 1987 and is headquartered in Luxembourg, Europe. The company offers a portfolio of over 130,000 analytical methods and more than 150 million assays performed each year to establish the safety, identity, composition, authenticity, origin, traceability, and purity of biological substances and products, as well as carry out human diagnostic services. The company has its geographic presence across 39 countries in Europe, North and South America, and Asia-Pacific.

5. GATC Biotech AG (Germany)

GATC Biotech AG was founded in 1990 and is headquartered in Constance, Germany. The company provides DNA and RNA sequencing and bioservices solutions to academics and industrial areas. It also provides next generation sequencing services including genomes, targeted (re)-sequencing, human sample sequencing, transcriptomes, metagenomes, regulomes, pre-sequencing, NGS barcode labels, and next generation sequencing technologies; and bioservices services, including bioservices tools, pipelines and workflows, compute resources, data analysis reports, and case studies. GATC Biotech AG operates as a subsidiary of Eurofins Scientific SE. It offers its products through distributors in Italy, Japan, Portugal, Spain, and the Czech Republic.

6. Macrogen, Inc. (South Korea)

Macrogen, Inc. was founded in 1997 and is headquartered in Seoul, South Korea. Macrogen, Inc. provides next generation sequencing services such as whole genome, de novo, exome, targeted, transcriptomics, metagenome, and epigenome sequencing. The company also provides a variety of services such as oligo synthesis, database construction, genome research, and bioservices analysis system consulting services. Macrogen, Inc. provides genome research services in Korea and internationally.

7. Genotypic Technology Pvt. Ltd. (India)

Genotypic Technology Pvt. Ltd. was incorporated in 1998 and is headquartered in Bangalore, India. Genotypic Technology is the first Genomics service provider in India providing Microarray, Next Generation Sequencing (NGS), Bioservices and solutions to domestic/ international pharma, biotech companies and academia. The company provides its services for protocol optimization, probe designing, array layouts, project designing, and nucleic acid analysis to in-depth analysis. Genotypic Technology has its geographic presence in North America, Europe, Asia Pacific, Middle East & Africa, and Latin America.

8. GENEWIZ, Inc. (U.S.)

GENEWIZ, Inc. was founded in 1999 and is headquartered in South Plainfield, New Jersey, the U.S.; The company is a leading provider of research service in the field of Next Generation Sequencing, Sanger DNA sequencing, sequencing of bacteria and phage, gene synthesis, DNA cloning, genomics including mutation analysis, single nucleotide polymorphism, and bioservices. GENEWIZ, Inc. has its geographic presence in U.S., China, Germany, France, Japan, and the U.K.

9. Beijing Genomics Institute (China)

Beijing Genomics Institute (BGI) is the world’s largest genomics organization and non-profit research institution that was founded in 1999 and is headquartered in Shenzhen, China. The Company provides a wide range of commercial next generation sequencing services and genetic tests for medical institutions, agricultural and environmental applications. The Company operates all across the globe through its subsidiaries, namely, BGI China (Mainland), BGI Asia Pacific, BGI Americas (North and South America) and BGI Europe (Europe and Africa).

10. SciGenom Labs Pvt. Ltd (India)

SciGenom Labs Pvt. Ltd was founded in 2010 and is headquartered in Cochin, India with offices in Chennai & Hyderabad in India, and San Francisco in the U.S. It is a Genomics R&D services company that provides genomic sequencing and NGS services to life sciences and healthcare businesses globally as well as academic and government institutions in India.

Popular mentions – MedGenome (India), DNA Link, Inc. (South Korea), Otogenetics Corporation (U.S.), Novogene Corporation (China), LGC Limited (U.K.), CD Genomics (U.S.), SeqLL, LLC (U.S.)