Tag: WGS

WGS Facilitates Gene Editing System Upgrade

Researchers at the Korean Institute of Life Sciences and Technology engineered an efficient, miniaturized CRISPR-Cas gene-editing system that may be more easily packed into vectors for clinical applications. Their system employs the Cas variant Cas12f1 with a guide RNA (gRNA) remodeled to mitigate off-target effects, a design that could potentially…

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Pacific Biosciences Makes Progress on Sequencer Development, Amends Invitae Deal

NEW YORK – Pacific Biosciences said on Wednesday that it has made progress on the development of two sequencing platforms and announced that it is amending payment terms for its collaboration with Invitae on a high-throughput whole-genome sequencer. The Invitae collaboration is one of three R&D projects PacBio officials mentioned…

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Programmer or Software Developer in Bioinformatics

Job:Programmer or Software Developer in Bioinformatics 0 Dr. Vikas Bansal’s research group (bansal-lab.github.io) in the School of Medicine at the University of California San Diego is looking for a programmer or software developer to advance the development of computational tools and methods for human genome analysis. Research in the group…

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sequencing – Interpreting ‘samtools mpileup’ output for multiple inputs

I would like to calculate sequencing coverage for a WGS project. Both long and short reads. I’ve used samtools as following: samtools mpileup -Q 1 -aa illumina_sorted.bam nanopore_sorted.bam > depth.txt Previously, when I used samtools depth instead, I only had the columns I was interested in (chromosome name / base…

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Postdoctoral Scientist – Bioinformatics and Integrative Genomics Research Cluster in , for Cedars-Sinai Medical Center

Details Posted: 26-Apr-22 Location: Nationwide Type: Full-time Salary: Open Internal Number: 20002022 At Cedars-Sinai, postdoctoral scientists and other junior researchers fulfill a critical role in expanding the horizons of medical knowledge through biomedical research. By hosting more than 100 postdocs, who conduct vital research and receive advanced training with expert…

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Postdoc / Research Scientist in Bioinformatics and Computational Genomics

Job Description Are you a computer geek with a strong interest in genomics? Do you want to use your computational skills to solve human diseases? At the Department of Neurology at Harvard Medical School and Brigham & Women’s Hospital, we have two vacant positions: postdoctoral fellow and research scientist in…

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long run-time and low CPU usage

Pindel: long run-time and low CPU usage 0 I’m trying to run Pindel on some 30x Illumina WGS data. I aligned reads with BWA-MEM, then sorted by co-ordinates and indexed them with Samtools. I also tried filtering the bam files with samtools -F 0x800 as suggested by another post. I…

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Bioinformatics Pipeline Development Engineer II at Personalis, Inc

Personalis, Inc. is a leader in advanced cancer genomics for enabling the next generation of precision cancer therapies and diagnostics. The Personalis NeXT Platform® is designed to adapt to the complex and evolving understanding of cancer, providing its biopharmaceutical customers and clinicians with information on all of the approximately 20,000 human genes,…

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Using mothur toolsuite on Galaxy to analyze microbial datasets : bioinformatics

Hi all, I am using the mothur toolsuite on Galaxy to attempt to process duodenal microbiome samples in humans. The datasets I am using are paired reads generated by WGS. I am directly following this guide: training.galaxyproject.org/training-material/topics/metagenomics/tutorials/mothur-miseq-sop/tutorial.html I’m stuck on the OTU Clustering section for my data samples, specifically the…

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Variant quality and filters on GATK HaplotypeCaller generated VCFs

Variant quality and filters on GATK HaplotypeCaller generated VCFs 0 Hi, I am analysing human WGS data to diagnose rare inherited diseases. I followed the GATK Best Practices Guidelines for “Germline short variants discovery” for single-sample data to generate a VCF using HaplotypeCaller. The guidelines then point to the use…

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Why did I achieve shorter than initial reads subset after aligned reads extraction.

Why did I achieve shorter than initial reads subset after aligned reads extraction. 1 Hello dear colleages! I have recently faced some problem. I have worked with long WGS reads. Firstly I have filtered the longest subset of reads, and aligned them to the custom sequence with several structural variants…

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Bioinformatics Research Assistant – Idealist

The Fund for Public Health in New York City (FPHNYC) is a 501(c)3 non-profit organization that is dedicated to the advancement of the health and well-being of all New Yorkers. To this end, in partnership with the New York City Department of Health and Mental Hygiene (DOHMH), FPHNYC incubates innovative public…

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Research Scientist, Bioinformatics on beHired.in

POSITION OVERVIEW: The Clinical Bioinformatics and Exploratory Analytics department at Gilead supports drug development and other business use cases by providing analytical, engineering, and visualization solutions for clinical and multi-omics data.  You will collaborate across functions to enable scientific and other business exploration and decision-making, including statistical analysis, genomic data…

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Placenta has clues for an early diagnosis of ASD

The researchers of the‘UC Davis MIND during their research they used the genomic sequencing to find a DNA methylation signature in the placenta of infants diagnosed with autism. This hallmark has been linked to early fetal neurodevelopment. Thanks to this study, a new human gene linked to fetal brain development…

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Simple DNA test could detect common neurological disorders, study says | Genetics

A simple test could end years of uncertainty for people with relatively common neurological conditions, new research has found. Historically, obtaining a definitive diagnosis for conditions including Huntingdon’s disease and some forms of amyotrophic lateral sclerosis has been difficult, because, although the cause of the symptoms is genetic, knowing which…

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rs9789283 RefSNP Report – dbSNP

Help Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When…

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Amur ide genome – assembly database

 Home Assembly GCA_900092035.1 Assembly ID: – Source: GenBank Assembly ( ID GCA_900092035.1 ) Description: – Molecule type: – Submitter: – Organism: – Synonyms: – Assembly type: – Assembly level: – Assembly method: – Genome representation: – Excluded from RefSeq: – RefSeq category: – GenBank assembly accession: – RefSeq assembly accession: – RefSeq…

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Efficiently merge two BAM files while retaining reads from only one file in overlapping regions

Efficiently merge two BAM files while retaining reads from only one file in overlapping regions 1 I have a WGS BAM file that is fairly large (>150GB) and a smaller BAM file (<5GB) with reads in a small 10Mbp region. I want to (efficiently) merge the two BAM files while…

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CNV calling for wgs of S. pombe

CNV calling for wgs of S. pombe 0 Hi, Can anyone help to do CNV calling of WGS data of S.Pombe? I have 1 normal sample and 3 samples treated with a suppressor. I used Control-FREEC but did not get the right result. Can anyone help, how to do germline…

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Roche hiring Sr Bioinformatics Scientist in Cambridge, Massachusetts, United States

SUMMARY We are seeking a talented and motivated Senior Bioinformatics Scientist who will be an integral member of the Sequencing team contributing to the support and development of ground-breaking next-generation sequencing (NGS) products. As a member of Roche’s Sequencing and Life Science (SLS), Scientific Support and Applications team, you will…

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Radboud University Medical Center Increases HiFi Sequencing Capacity with PacBio’s Sequel IIe

Added whole genome sequencing capacity enables the SOLVE-RD research program to significantly increase sample throughput MENLO PARK, Calif., Jan. 07, 2022 (GLOBE NEWSWIRE) — PacBio (Nasdaq: PACB), a leading developer of high-quality, highly accurate sequencing platforms, today announced Radboud University Medical Center (Radboudumc) in Nijmegen, the Netherlands will increase their…

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Comparison of CNV analysis methods: Array CGH vs NGS

Rare genetic disorders are caused by variants in major functional genes. Most are SNV or INDEL variants, but SVs, such as CNVs or chromosomal variants, can also be the cause. Recently, a large-scale study has also been published showing that CNVs were identified in 11-12% more infants and children with…

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Index of /refseq

Name Last modified Size Parent Directory – B_taurus/ 2020-02-25 11:45 – D_rerio/ 2020-02-25 11:46 – FunctionalElements/ 2020-08-13 18:17 – H_sapiens/ 2020-02-25 11:39 – LocusLink/ 2007-04-27 08:08 – MANE/ 2021-06-16 13:56 – M_musculus/ 2020-07-17 15:40 – R_norvegicus/ 2020-02-25 11:44 – S_scrofa/ 2020-02-25 11:44 – TargetedLoci/ 2016-08-09 11:27 – X_tropicalis/ 2020-02-25 11:45…

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Postdoctoral Scholar – Bioinformatics/Biomedical Data Science

The University of Nevada, Reno (UNR) appreciates your interest in employment at our growing institution. We want your application process to go smoothly and quickly. Final applications must be submitted prior to the close of the recruitment. If you need assistance or have questions regarding the application process, please contact…

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Bioinformatics Analyst in Evanston, IL for Northwestern University

Details Posted: 23-Dec-21 Location: Evanston, Illinois Salary: Open Categories: Information Technology Staff/Administrative Department: MED-Center for Genetic MedSalary/Grade: EXS/8 Job Summary: Partners with clients to design, develop, implement and maintain business solutions regarding data management and analysis.  This includes database administration, data consolidation, data analysis and management reporting.  Utilizes software to…

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Scientists Develop $10 Per Genome Approach for Large-Scale Bacterial Sequencing

A worldwide consortium of scientists, led by the Earlham Institute and the University of Liverpool, has developed an efficient, inexpensive approach to large-scale bacterial genome sequencing that could equip researchers in low- and middle-income countries (LMICs) with cheap and accessible methods for sequencing large collections of bacterial pathogens—at a cost…

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bedtools genomecov problem with merged bam

Hi, I was using puge haplotig, and in that work flow the first step was to use bedtools genomecov so I moved here. I have three paired end dataset, illumina wgs reads, HiC reads, and Chicago sequencing reads. I aligned the paired end reads of illumina wgs to the genome,…

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Benchmarking the NVIDIA Clara Parabricks germline pipeline on AWS

This blog post was contributed by Ankit Sethia, PhD, and Timothy Harkins, PhD, at NVIDIA Parabricks, and Olivia Choudhury, PhD,  Sujaya Srinivasan, and Aniket Deshpande at AWS. This blog provides an overview of NVIDIA’s Clara Parabricks along with a guide on how to use Parabricks within the AWS Marketplace. It…

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Postdoctoral Scholar in Microbiology and Bioinformatics, Cumming School of Medicine – University of Calgary – job portal

University of Calgary Home Prospective Students Current Students Alumni Community Faculty & Staff Home Information for Candidates Opportunities by Type Opportunities by Faculty/Unit Home Information for Candidates Opportunities by Type Opportunities by Faculty/Unit Share this Job: Postdoctoral Scholar in Microbiology and Bioinformatics, Cumming School of Medicine Job ID: 24643 Updated:…

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Novo Nordisk hiring Scientist I – Bioinformatics in Seattle, Washington, United States

About The DepartmentAt Novo Nordisk Research Center Seattle, Inc. (NNRCSI) our scientists apply cutting-edge technologies to early R&D projects with the goal of bringing real change to People with Diabetes and Obesity. Your skills, dedication and ambition will help change lives for the better and you will work with extraordinary…

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What is the procedure for the assembly of bacteriophage genomes?

What is the procedure for the assembly of bacteriophage genomes? 0 Hello, is the assembly of bacteriophages’ genome different from that of humans? I understand that it is common to use NGS to sequence the genomes of newly isolated bacteriophages, but what is the correct procedure? When isolating a new…

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Kraken2

Kraken2 0 I wanted to make a kraken database but i got this error while running the command.I am using Kraken2 $ kraken2-build –standard –threads 24 –db kraken2database/ Downloading nucleotide gb accession to taxon map… done.Downloading nucleotide wgs accession to taxon map… done.Downloaded accession to taxon map(s)Downloading taxonomy tree data……

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Genomic Characterization of Clinical Listeria monocytogenes Isolates in Beijing, China

Listeria monocytogenes is a foodborne human pathogen that affects public health worldwide. Whole-genome sequencing (WGS) can classify L. monocytogenes isolates and identify virulence islands and resistance genes potentially influencing infectivity. Herein, WGS was used to assess 151 L. monocytogenes isolates from 120 cases of clinical infection in Beijing, China, between…

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How to call LOH with FreeC

How to call LOH with FreeC 0 Good morning, I am try to infer loss of heterozygosity (LOH) from WGS data using Freec. For this purpose, I am using these parameters in the “[BAF]” section of the configuration file: [BAF] makePileup = My_somaticVCF.vcf.gz fastaFile = hg19.fa SNPfile = hg19_snp142.SingleDiNucl.1based.txt.gz When…

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Bioinformatics postdoctoral position

Bioinformatics postdoctoral position There is an immediate opening for a bioinformatics postdoctoral position in Tahlan Laboratory at the Department of Biology (www.mun.ca/faculty/ktahlan/index.php) to study the epidemiology and evolution of mycobacterial pathogenesis using whole genome sequencing (WGS, Illumina) data. Responsibilities: Bioinformatics analysis of WGS DNA-seq data. Writing results for publication. Qualifications:…

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Ethnic Diversity of DPD activity and the DPYD Gene

Plain Language Summary Fluoropyrimidine (FP; 5-FU, capecitabine) is a common chemotherapy used to treat many different cancers, including cancer of the colon and rectum, upper digestive tract, breast and head and neck. Cancer patients who receive FP chemotherapy are at risk of developing severe side effects from their treatment. A…

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Galaxy Europe | Accessible and scalable detection and identification of foodborne pathogens, a project with Biolytix and funded by EOSC-Life

TLDR: Thanks to funding from EOSC-Life, the Freiburg Galaxy team will work in 2022 with Biolytix, a Swiss Small and Medium-sized Enterprise (SME) specialized in molecular biology and microbiological analyses, toward Accessible and scalable detection and identification of foodborne pathogens. Background Food contaminations with pathogens are a major burden on…

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Next Generation Sequencing Industry to Cross $34.8 Billion by 2027

DUBLIN, Dec. 8, 2021 /PRNewswire/ — The “Next Generation Sequencing Market, Global Forecast, Impact of COVID-19, Industry Trends, Growth, Opportunity By Types of Test, Company Analysis” report has been added to ResearchAndMarkets.com‘s offering. According to the report, the Global Next Generation Sequencing Market will reach US$ 34.8 Billion by 2027….

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Lee Placito Fellowship in Bioinformatics

Job Details Lee Placito Fellowship in Bioinformatics Nuffield Department of Surgical Sciences, Old Road Campus Research Building, Headington, Oxford Grade 7: £33,309 – £40,927 per annum Contract type: Fixed term for 3 years Hours: Full-time About the role We are looking for an enthusiastic bioinformatician who has an interest in…

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Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology

Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands Wouter van Rheenen, Rick A. A. van der Spek, Mark K. Bakker, Joke J. F. A. van Vugt, Paul J. Hop, Ramona A. J. Zwamborn, Annelot M. Dekker, Klara Gawor, Henk-Jan Westeneng, Gijs H. P. Tazelaar, Kristel R. van Eijk, Maarten Kooyman, Ewout J. N. Groen, Michael…

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Are there some methods can be used to do association analysis in a very small size group?

Are there some methods can be used to do association analysis in a very small size group? 0 Sorry that I’m not native English speaker, so maybe I did not make myself clear somewhere. If so, please forgive me and welcome to ask. we foung a new trait in our…

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Salmonella outbreak detected in half of US states

The Centers for Disease Control and Prevention (CDC) warned Friday that an outbreak of salmonella due to an “unknown food source” has been detected in 25 states across the U.S. The agency said that on Sept. 2, it identified an outbreak of 20 salmonella oranienburg infections and that, since then,…

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Filter criteria for variants based on GBS data

Filter criteria for variants based on GBS data 0 Are there recommended filter criteria for variants based on GBS data? I currently use this filter formula that is used in bcbio for WGS based variants soft-filtering bcftools –soft-filter GATKCutoffSNP -e TYPE=”snp” && (MQRankSum < -12.5 || ReadPosRankSum < -8.0 ||…

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How to transform a whole-genome callset into whole-exome callset?

How to transform a whole-genome callset into whole-exome callset? 0 Hi all, I have a callset from whole-genome data and with this callset, I want to transform it into exome callset by extracting the variants using a exome target interval. I obtained two exome target list, one from 1KG project…

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Mystery Salmonella Outbreak Strikes 127 People From 25 States, CDC Still Investigating Potential Source

The Centers for Disease Control and Prevention (CDC) has once again identified a multi-state Salmonella outbreak in the country this year. The last reported disease outbreak was caused by Salmonella typhimurium and Salmonella infantis identified in Italian deli meats, such as salami, and prosciutto. The Denver Channel reported that the recent Salmonella outbreak…

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How to access WGS files on TCGA for melanoma/SKCM

How to access WGS files on TCGA for melanoma/SKCM 0 I was trying to find WGS files for TCGA-SKCM so I can run WGS files through our pipeline and search for circular DNA elements in melanoma samples. However, looking on the TCGA website for this type of cancer, it’s unclear…

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The faces of three ancient Egyptians appeared thanks to the remains of DNA more than 2,000 years ago

The faces of three ancient Egyptians are brought back to life thanks to DNA group of scientists Recreate The faces of three ancient Egyptian men using DNA that is more than 2,000 years old. According to the magazine NEWSWEEKIt is believed that this is the first time that modern techniques…

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Mystery Salmonella Oranienburg Outbreak strikes 127 in 25 states

Likely linked to restaurant exposures – Texas hardest hit. On September 2, 2021, CDC identified an outbreak of 20 Salmonella Oranienburg infections. Since then, the outbreak has grown rapidly. As of September 15, 2021, 127 people infected with the outbreak strain of Salmonella Oranienburg have been reported from 25 states….

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Genomic features of a carbapenem-resistant K. oxytoca strain

Introduction Antimicrobial resistance is a global issue associated with an increased and often unrestricted antibiotic use in clinical settings, which leads to the dissemination of carbapenem-resistant Enterobacterales (CRE) in healthcare facilities (World Health Organization, 2017).1 CRE constitutes a large group of bacteria with different mechanisms for drug resistance. Among them,…

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Phylogeographic reconstruction of the marbled crayfish origin

Procambarus fallax collections and PCR genotyping Animals were collected from various wild populations (Table S1) in compliance with state and local regulations (Georgia department of natural resources scientific collection permit 115621108, state of Florida collection permits S-19-10 and S-20-04). DNA was isolated from abdominal muscle tissue using SDS-based extraction and precipitation…

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New publication in European Urology demonstrates value of PredicineCARE liquid biopsy test for monitoring PD-L1 immunotherapy in patients with metastatic prostate cancer | News

HAYWARD, Calif., Sept. 16, 2021 /PRNewswire-PRWeb/ — Predicine, Inc. announced today results from a liquid biopsy study demonstrating the clinical application of utilizing the PredicineCARE liquid biopsy NGS assay to serially monitor changes in ctDNA levels in patients with metastatic castration-resistant prostate cancer (mCRPC). The European Urology study evaluated the effects…

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Faces of Three Ancient Egyptians Brought to Life Using 2,000-Year-Old DNA

The faces of three ancient Egyptian men have been brought to life by scientists, using DNA that is more than 2,000 years old. This is thought to be the first time modern techniques have been used on human DNA of this age, with the trio of samples estimated to be…

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Principal Bioinformatics Scientist Job Opening in San Diego, CA at DermTech

About DermTech: At DermTech, we believe there’s a better way to treat your skin, and we’re using technology, innovation, and data to fundamentally change the way the world practices dermatology. We have developed technology that assesses your skin at the RNA and DNA level, so we can see signs of…

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Parabon Recreates Egyptian Mummy Faces From Ancient DNA

New Snapshot methods for low-coverage sequencing bring hidden data to life Scientific Poster Image Scientific Poster Image Scientific Poster Image RESTON, Va., Sept. 15, 2021 (GLOBE NEWSWIRE) — At the 32nd International Symposium on Human Identification (ISHI), being held this week in Orlando, Florida, Parabon NanoLabs will unveil for the…

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compare SV results across samples

compare SV results across samples – Manta, Delly 3 Hi folks, I have Delly and Manta results for a cohort of WGS tumour libraries. Some of the libraries are derived from the same sources using different methods in the lab and I want to be able to compare/contrast the sets…

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Genomic and phenotypic characteristics for Vibrio vulnificus

Background Fisheries and aquaculture are becoming increasingly intensive to meet recent human consumption, resulting in proliferation of marine pathogens and food security concerns.1,2 Vibrio species, as one of the most dangerous foodborne pathogens, cause vibriosis in human around the world.3 It has been reported that vibriosis resulted in 80,000 illnesses…

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ABRF Study Benchmarks NGS Platforms on Human, Microbial Samples, Provides Peek at Genapsys Data

NEW YORK – The results of a major, core facilities-driven benchmarking study for next-generation sequencing platforms are in, and just about every major player in the field can claim a victory of some sort. The data support longstanding advantages touted by market leader Illumina, while also providing a sneak peak…

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Research questions regarding WGS data from plant pathogens

Research questions regarding WGS data from plant pathogens 1 If you have a specific problem to solve, random experts strangers on the internet will likely be able to help. I think that’s where this forum is most useful. When it comes to big career questions such as the one you…

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How does one harmonize WGS data with Microarray data?

How does one harmonize WGS data with Microarray data? 0 Hello all, I’ve been working with microarray data which, of course, explicitly reports the genotype at each SNP on the microarray chip Now I am trying to incorporate WGS datasets into my project, and I would like to extract the…

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Nature Papers Examine Factors Affecting Mutation Detection, Map of Development, Sequencer Performance

An examination of how aspects of the sequencing and analysis process can influence efforts to detect cancer mutations in clinical samples is reported in Nature Biotechnology this week, highlighting the need for reproducibility and accuracy in precision oncology. While the falling costs of next-generation sequencing have led to a rise…

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Bioinformatics (HEO) Jobs in London at Public Health England –

The Bioinformatics and Whole Genome Sequencing (WGS) Software Development unit is part of Data Analytical Sciences within PHE’s National Infection Service Division. The unit is globally pre-eminent in the design, construction, validation and deployment of bioinformatics pipelines for the automated analysis of Next Generation Sequencing (NGS) whole Genome Sequence (WGS)…

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Principal Software Engineer 1 – Bioinformatics Job in California

Summary: Our engineering team specializes in developing a fast and accurate FPGA-accelerated platform called DRAGEN, for the secondary analysis of NGS data. Team activities are two-fold: 1) algorithm design of analysis methods to discover variants, and, 2) highly-efficient HW/SW implementation for fast run time. The platform covers a wide…

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Any suggestion on metagenomics pipelines for processing shotgun metagenomics whole genome sequencing samples?

Any suggestion on metagenomics pipelines for processing shotgun metagenomics whole genome sequencing samples? 0 Hi, I have some shotgun metagenomics gonorrhea samples and I want to use metagenomics pipeline to process the samples and then detect antimicrobial resistance. I looked into few pipelines so far for metagenomics data such as…

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Senior Bioinformatics Scientist job with Paramount Recruitment

Senior Bioinformatics Scientist *The company is offering flexible working options* I am working with a biotech company in Cambridge who is looking for a Senior Bioinformatics Scientist to join their growing Bioinformatics team. The company focus on identifying and developing cancer treatments by exploiting targets within DNA damage response (DDR)….

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Bioinformatics Analyst I – Job at Medical College of Wisconsin in Milwaukee, WI

Position Description: Every great life-changing discovery begins the same way-with new knowledge. It can change everything, from a single life to the future of entire communities. That’s why academic medicine, and the continuous pursuit of knowledge, is at the center of everything we do…

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Is there way to get genbank assembly id from nuccore id using ncbi eutils ?

Is there way to get genbank assembly id from nuccore id using ncbi eutils ? 2 Hello, I am trying to get the assembly id (for eg. GCA_000312685.1 ) for the nuccore id (CP003157.1) using eutils? For the WGS nuccore id such as CAJY00000000 you can get the the assembly…

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Genomic Analysis of Lung Cancer in Never Smokers Identifies Three Molecular Subtypes

A genomic analysis of lung cancer in people with no history of smoking has found that a majority of these tumors arise from the accumulation of mutations caused by natural processes in the body. The international team of scientists, led by researchers at the National Cancer Institute (NCI), carried out…

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Has anyone here used the MAC tool for merging assemblies?

Has anyone here used the MAC tool for merging assemblies? 0 I’m relatively new to whole genome work and have been exploring various tools for assembling/mapping genomes. I’ve read that not all assembly tools/programs are created equal and often times it is valuable to assess assemblies from multiple tools for…

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Use of GenotypeGVCFs in population genetic studies

Use of GenotypeGVCFs in population genetic studies 0 I have 16 whole genome sequenced samples from two populations (8 for each population). My goal is detection of signature of selection and introgression. I performed read cleaning, mapping to reference, mark duplication. SNP calling was performed using HaplotypeCaller in GATK for…

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Paired-end reads reported without mates: how to play matchmaker?

Hi Everyone, I am currently looking at Acute Myeloid Leukemia (AML) paired-end WGS samples from the TARGET data ocg.cancer.gov/programs/target/target-methods#3241. A bioinformatician in our group remapped the samples from hg19 to hg38. Unfortunately, we do not have any copies of the hg19 version anymore. However, when I try to run anything…

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How to pass custom software specific variables to nf-core/sarek nextflow pipeline?

How to pass custom software specific variables to nf-core/sarek nextflow pipeline? 0 I’m attempting to call whole genome variants using nf-core/sarek nextflow pipeline. In QC step there is an option that invokes trim_galore quality trimming, but i don’t know how to pass my custom adapters to be cut as well….

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How to filter GATK vcf file using other programs

How to filter GATK vcf file using other programs 0 hi everyone I called variants for a WGS project using GATK (HaplotypeCaller). Now, when I want to filter that VCF file by VariantFiltration command in GATK, so the following error message appears. java.lang.NumberFormatException: For input string: “10.90” I asked my…

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Tool for calculating base-level error rate in WGS.

Tool for calculating base-level error rate in WGS. 0 I am seeking a tool to calculate substitution, insertion, deletion error rates at a per-base sequenced level. It has to take a genomic region bed file and vcf files since I don’t want to count germline variants and would like to…

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Defects in 8-oxo-guanine repair pathway cause high frequency of C > A substitutions in neuroblastoma

Significance The collection of large amounts of whole-genome sequencing data allowed for identification of mutational signatures, which are characteristic combinations of substitutions in the context of neighboring bases. The clinical significance of these mutational signatures is still largely unknown. In neuroblastoma, we showed that high levels of cytosine > adenine…

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Research Scientist Bioinformatics at Exscientia

We are looking to hire an experienced bioinformatician who specializes in the analysis of human NGS data. The Research Scientist Bioinformatics will lead the development and expansion of our in-house NGS capabilities together with data managers and software developers, while also carrying out project-specific analyses. Exscientia GmbH is a company…

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Case Control count per variant

Case Control count per variant 0 Hi, I was wonder if there was any software out there that will count the number of samples in a group that are homozygous ref, heterozygous, or homozygous for a variant an output result in a text file? In the past, I have been…

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featureCounts for WGS instead of RNA-seq

featureCounts for WGS instead of RNA-seq 1 Hello all, I have done whole genome sequencing and aligned reads on a reference genome. I have some bam files. I want to get the number of reads mapped to sepecific regions defined in a gff3 files. I have used featureCounts for RNA-seq…

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Bioinformatics Scientist (Open Level) – Bild Laboratory job with City of Hope

Thank you for your interest. Please note, the purpose of this posting is to recruit for on-going and future positions. About City of HopeCity of Hope, an innovative biomedical research, treatment and educational institution with over 6000 employees, is dedicated to the prevention and cure of cancer and other life-threatening…

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Basepaws seeks partnerships with veterinary hospitals to propel feline health

The pet biotechnology company is looking to collaborate with veterinary clinics to help advance its research studies focusing on areas of unmet needs in feline health. Basepaws is in the process of developing a unique category of screening tools that will combine genomic, microbiome, and health history data to identify…

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Is it possible to detect of SNVs and InDels in low coverage WGS (5-10X) data?

Is it possible to detect of SNVs and InDels in low coverage WGS (5-10X) data? 2 Hello, the Biostar community, What I know about low coverage WGS (or shallow WGS) data is that it is an economic technique for genomic copy number detection in the realms of tumor diagnosis or…

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Multiform antimicrobial resistance from a metabolic mutation

Abstract A critical challenge for microbiology and medicine is how to cure infections by bacteria that survive antibiotic treatment by persistence or tolerance. Seeking mechanisms behind such high survival, we developed a forward-genetic method for efficient isolation of high-survival mutants in any culturable bacterial species. We found that perturbation of…

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The Biostar Herald for Friday, August 27, 2021

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…

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best automated method (unix commandline) to get genome-assembly-accession number for given protein-accession-number (ncbi)

best automated method (unix commandline) to get genome-assembly-accession number for given protein-accession-number (ncbi) 1 What would be the best way (if there is any) to get the accession number of a genome assembly that contains a given protein accession number? E.g. if i just have the results of a blastp…

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Head of Bioinformatics job in Princeton, NJ | GENMAB A/S

Genmab is focused on the creation and development of innovative and differentiated antibody products, with the aim of improving the lives of cancer patients. The Role The successful candidate will lead the global bioinformatics function and be responsible for many aspects of data including architecture, access, classification, standards, integration, pipelines…

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the Genomic Rearrangement IDentification Software Suite

Tool:GRIDSS: the Genomic Rearrangement IDentification Software Suite 0 GRIDSS is typically used for detecting structural variation breakpoints from short read sequencing data but is a modular software suite containing a number of tools useful for the detection of genomic rearrangements including: A structural variant caller. The GRIDSS caller uses break-end…

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Dante vs Nebula indexcov

Dante vs Nebula indexcov 0 I’m trying to understand the variance of the same individual on the same chromosomes tested on Dante 30x and Nebula 100x. Is this expected? Other chromosomes are not as drastic. Which WGS is more “the truth” ? dante nebula indexcov • 27 views Login before…

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WGS bacterial metagenomic pipeline – group comparison

WGS bacterial metagenomic pipeline – group comparison 0 Hello all, I was wondering what’s the recent state-of-the-art pipeline to do metagenome comparison, with multiple samples and groups? E.g. I have several “patients” and several “controls” in the form of WGS reads, and I want to run a comparison (on some…

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Platypus

Platypus 0 Hi, I’m super new to WGS and bioinformatics, but I’m a classic software data scientist, so I know enough to be annoying. I’m using Platypus too call variants on 100X WGS via Nebula Genomics. I found an odd series of calls and am not sure if this is…

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Where do I get a WES dataset of size

Where do I get a WES dataset of size <1GB 1 Can someone please tell me from where can I get the WES or WGS dataset of size <1GB WGS WES genomics • 164 views Just browse sra-explorer.info for datasets. I doubt you can meaningfully query for file size as…

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Making a living with bioinformatics

Please do not find this offensive in any way. Please do not get discouraged by this post. I mean nothing bad by this post. I just need some advice as lately (for a year now) I am finding it very difficult to “see the light at the end of the…

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Allele-Specific analysis for human WGBS data

Allele-Specific analysis for human WGBS data 0 Hi everyone, I need to perform allele-specific methylation analysis for human whole genome bisulfite sequencing data. As Allele-specific analysis is dependent on SNPs/Polymorphic sites, I stuck with two queries: Is there a way to get these polymorphic sites from WGBS data ? (I…

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VCF Filter On Small Genomes

VCF Filter On Small Genomes 0 Hi guys, I am working on a yeast species (Candida glabrata) NGS data to find any mutations related to drug resistance. I am new in bioinformatics so I am using Galaxy.eu to get use to algorithms. There is literature about some genes that mutations…

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