<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/44229?offset=50 https://bioinformaticsonline.com/opportunity/view/38815/research-opening-ibab-bengaluru Mon, 28 Jan 2019 17:45:54 -0600 <![CDATA[Research opening @ IBAB, Bengaluru]]> 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/

]]> https://bioinformaticsonline.com/bookmarks/view/39674/simka-and-simkamin-are-comparative-metagenomics-method-dedicated-to-ngs-datasets Sat, 06 Jul 2019 13:56:10 -0500 https://bioinformaticsonline.com/bookmarks/view/39674/simka-and-simkamin-are-comparative-metagenomics-method-dedicated-to-ngs-datasets <![CDATA[Simka and SimkaMin are comparative metagenomics method dedicated to NGS datasets]]> 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

]]> Neel https://bioinformaticsonline.com/pages/view/40228/bioinformatics-services-cro-services Wed, 06 Nov 2019 00:33:11 -0600 https://bioinformaticsonline.com/pages/view/40228/bioinformatics-services-cro-services <![CDATA[Bioinformatics Services / CRO Services]]> RASA is set to provide premium technical and scientific services in a form of solutions, product development and training. .We are also very proficient in providing the high quality Research & Development services in life science informatics field like Next Generation Sequencing (NGS) Data Analysis,Computational Drug Discovery, Bioinformatics, Chemo-informatics and BIO-IT.

RASA offers faster, better and cost effective cutting edge technology solutions to chemical and life science research and industry. We provide our customers with A seamless model of wide expertise and comprehensive platforms. Our Value is to take our customers

]]> RASA Life Sciences https://bioinformaticsonline.com/bookmarks/view/40604/gapfinisher-a-reliable-gap-filling-pipeline-for-sspace-longread-scaffolder-output Fri, 24 Jan 2020 06:04:40 -0600 https://bioinformaticsonline.com/bookmarks/view/40604/gapfinisher-a-reliable-gap-filling-pipeline-for-sspace-longread-scaffolder-output <![CDATA[gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output]]> gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines. They compare the performance of gapFinisher against two other published gap filling tools PBJelly and GMcloser.

gapFinisher can fill gaps in draft genomes quickly and reliably.

Address of the bookmark: https://github.com/kammoji/gapFinisher

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/41146/lofreq-a-sequence-quality-aware-ultra-sensitive-variant-caller-for-ngs-data Tue, 18 Feb 2020 03:24:22 -0600 https://bioinformaticsonline.com/bookmarks/view/41146/lofreq-a-sequence-quality-aware-ultra-sensitive-variant-caller-for-ngs-data <![CDATA[LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data]]> LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty), which are usually ignored by other methods or only used for filtering.

https://github.com/CSB5/lofreq

http://csb5.github.io/lofreq/installation/

https://github.com/CSB5/lofreq/tree/master/dist

Address of the bookmark: http://csb5.github.io/lofreq/

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/42917/fings-filters-for-next-generation-sequencing Sat, 27 Feb 2021 01:18:35 -0600 https://bioinformaticsonline.com/bookmarks/view/42917/fings-filters-for-next-generation-sequencing <![CDATA[FiNGS: Filters for Next Generation Sequencing]]> Key features
  • Filters SNVs from any variant caller to remove false positives
  • Calculates metrics based on BAM files and provides filtering not possible with other tools
  • Fully user-configurable filtering (including which filters to use and their thresholds)
  • Option to use filters identical to ICGC recommendations

FiNGS provides researchers with a tool to reproducibly filter somatic variants that is simple to both deploy and use, with filters and thresholds that are fully configurable by the user. It ingests and emits standard variant call format (VCF) files and will slot into existing sequencing pipelines. It allows users to develop and implement their own filtering strategies and simple sharing of these with others.

FiNGS reliably improves upon the precision of default variant caller outputs and performs better than other tools designed for the same task.

Address of the bookmark: https://github.com/cpwardell/FiNGS

]]> Neel https://bioinformaticsonline.com/news/view/34711/1mb-long-dna-with-nanopore-technology Tue, 19 Dec 2017 18:49:28 -0600 https://bioinformaticsonline.com/news/view/34711/1mb-long-dna-with-nanopore-technology <![CDATA[1mb long DNA with Nanopore technology]]> The first continuous DNA read of more than a million bases (>1Mb) has been achieved, using Oxford Nanopore sequencing technology. Congratulations to Martin Smith and collaborators! Read more: http://bit.ly/2j5TNCO

]]> Jit https://bioinformaticsonline.com/bookmarks/view/37835/variantbam-filtering-and-profiling-of-next-generational-sequencing-data-using-region-specific-rules Thu, 04 Oct 2018 16:30:44 -0500 https://bioinformaticsonline.com/bookmarks/view/37835/variantbam-filtering-and-profiling-of-next-generational-sequencing-data-using-region-specific-rules <![CDATA[VariantBam: Filtering and profiling of next-generational sequencing data using region-specific rules]]> VariantBam is a tool to extract/count specific sets of sequencing reads from next-generational sequencing files. To save money, disk space and I/O, one may not want to store an entire BAM on disk. In many cases, it would be more efficient to store only those read-pairs or reads who intersect some region around the variant locations. Alternatively, if your scientific question is focused on only one aspect of the data (e.g. breakpoints), many reads can be removed without losing the information relevant to the problem.

 

Address of the bookmark: https://github.com/broadinstitute/VariantBam

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/38535/nanopack-visualizing-and-processing-long-read-sequencing-data Tue, 25 Dec 2018 21:20:50 -0600 https://bioinformaticsonline.com/bookmarks/view/38535/nanopack-visualizing-and-processing-long-read-sequencing-data <![CDATA[NanoPack: visualizing and processing long-read sequencing data]]> Address of the bookmark: https://github.com/wdecoster/nanopack

]]> Jit https://bioinformaticsonline.com/bookmarks/view/40544/ngs-bits-short-read-sequencing-tools Thu, 16 Jan 2020 23:14:00 -0600 https://bioinformaticsonline.com/bookmarks/view/40544/ngs-bits-short-read-sequencing-tools <![CDATA[ngs-bits - Short-read sequencing tools]]> Binaries of ngs-bits are available via Bioconda. Alternatively, ngs-bits can be built from sources:

Address of the bookmark: https://github.com/imgag/ngs-bits

]]> Neel