Tag: WGS

Getting information on CRAM files from headers inside the files 1 Hello. I wish to know if one can find the following information in CRAM files’ headers: 1) Whether or not sequencing data in CRAM files is from WGS or WES, and if so, where? and 2) In case one…

Scientist, Bioinformatics – ChIP-seq, RNA-seq, Hi-C, ATAC-seq, WGS, Exome-seq This Jobot Job is hosted by: Emmet NittoAre you a fit? Easy Apply now by clicking the “Apply Now” button and sending us your resume.Salary: $90,000 – $115,000 per year A bit about us: Based in Carlsbad, CA, we are a…

Pune, Maharashtra, India, November 15 2022 (Wiredrelease) Mrfactors.com –:The Global DNA Sequencing Market is estimated to be USD 4581.2 million in 2022 and is expected to reach USD 16915.22 million by 2033, growing at a CAGR of 11.5%. DNA sequencing is the process of determining a DNA segment’s nucleotide sequence….

At Cedars-Sinai,postdoctoral scientists and other junior researchers fulfill a critical role inexpanding the horizons of medical knowledge through biomedical research. Byhosting more than 100 postdocs, who conduct vital research and receive advancedtraining with expert faculty mentors, Cedars-Sinai supports theongoing medical education process that continues beyond PhD/MD graduation.   Overview: Bioinformaticsand Integrative Genomics  …

ABSTRACT: Whole Genome/Exome Sequencing (WGS/WES) data and Electronic Health Records (EHRs), such as large scale national and institutional biobanks, have emerged rapidly worldwide. In this talk, I will discuss the analytic tools and resources for scalable analysis of large scale biobank- and population-based Whole Genome Sequencing (WGS) association studies of…

Find ~1 Mb regions of genome that are shared by two or more WGS samples? 0 Hello, I have 12 WGS samples that are part of a big pedigree, I need to pinpoint genomic regions ~1 Mbp that are identical between some or many or all of them. I’ve never…

Detecting de novo SNV with vcftools 1 Hi, all. I have a raw whole genome sequence data of a kind of fish trio: father, mother and offspring. I would like to know how many SNV loci there are in the child but not in the parent (i.e. de novo SNV…

Serratia marcescens can cause a range of severe infections and contributes to nosocomial outbreaks. Although whole-genome sequencing (WGS)-based typing is the standard method for molecular surveillance and outbreak investigation, there is no standardized analytic scheme for S. marcescens core genome multilocus sequence typing (cgMLST). Here, the development and evaluation of…

Responsibilities Requisition # 20002022A 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 faculty mentors, Cedars-Sinai supports the ongoing medical education process that continues…

Login page for ncbi wgs portal is presented below. Log into ncbi wgs portal page with one-click or find related helpful links. Last Updated: 17th August, 2022 WGS – NCBI – NIH   www.ncbi.nlm.nih.gov/genbank/wgs Nov 13, 2017 – Whole Genome Shotgun (WGS) projects are genome assemblies of incomplete genomes or…

Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, US Usman A. Tahir, Daniel H. Katz, Jeremy M. Robbins, Zsu-Zsu Chen, Mark D. Benson, Daniel E. Cruz, Debby Ngo, Shuliang Deng, Xu Shi, Shuning Zheng, Aaron S. Eisman, Laurie Farrell, James G. Wilson & Robert E. Gerszten Broad Institute of Harvard and MIT, Cambridge, MA, US Julian Avila-Pachecho, Alexander G….

Study population The study sample included 34,072 unrelated (3rd degree or less) TOPMed participants from eight U.S. based cohort studies: Jackson Heart Study (JHS; n = 2504), Framingham Heart Study (FHS; n = 3520), Hispanic Community Health Study/Study of Latinos (HCHS/SOL; n = 6,408), Atherosclerosis Risk in Communities study (ARIC; n = 6197), Cardiovascular Health Study (CHS; n = 2835),…

Details Posted: 11-Aug-22 Location: Cincinnati, Ohio Salary: Open Categories: Academic / Research Description Computational postdoctoral positions in bioinformatics and epigenomics (computational/experimental) are available at Dr.Yaping Liu’s lab in the Division of Human Genetics. One of the research directions in Dr. Liu’s group is to study single-cell multi-omics data to understand…

Forum:Why isn’t GWAS used in oncology? 1 From what I can gather, GWAS is not used in oncology because ~ cancer is characterized by rare/ random mutations that amount to an overall burden on the genes that they up/down regulate. Is this assumption correct? gwas association oncology studies somatic cancer…

Sequence analysis of 131 human brains has revealed the mutagenesis processes that take place throughout life, from development to senescence. In a new study published in the July 29, 2022, issue of Science, the authors described how high rates of brain somatic mutations (what they call hypermutability) correlated with age….

Abstract We previously reported highly specific genome editing in rice by CRISPR-Cas9 and Cas12a with single DNA double strand break (DSB) (Tang et al., 2018). Two concurrent DSBs by CRISPR-Cas9 could generate defined deletions (Zhou et al., 2014), inversions (Schmidt et al., 2020), and translocations (Beying et al., 2020). Off-target…

Bayes–Central Singapore The ideal candidate will have an established track record in the field of structural biology, molecular dynamics and possess a broad base… National Cancer Centre Singapore–Outram We are recruiting Bioinformatics Specialists and Postdoctoral Fellows at the Cancer Discovery Hub, National Cancer Centre Singapore. You… $1,000 – $1,000 per…

Position summary As a Senior Bioinformatics Scientist, you will provide bioinformatics support for product research and development, as well as the marketing, sales and on-market product support teams. You will collaborate and innovate with bioinformatics scientists, software engineers and  molecular biologists to build products that will impact patient care for…

Detecting heterogeneous X chromosome counts in XXY individual 1 Hi, I have a WGS of an individual with XXY DNA. I’d like to analyze their X calls to see what percentage are heterogeneous vs homogenous. I don’t know what tool is the best for this. Any suggestions would be really…

At CircaGene, we analyze the whole encyclopedia (Whole Genome Sequencing – a 99.9% accuracy) reading all pages several times (10x, 15x, 30x). Competitors only look at some volumes (chromosomes) missing a lot of mutations, making them not accurate. Majority of our competitors uses genotyping technique instead of WGS; with their…

Job description Location: Boca Raton, Florida Job Description: The College of Medicine of Florida Atlantic University, the 5th public university in Florida, is seeking a Bioinformatics Postdoctoral Associate with experience in bioinformatics pipeline development and genomics data analysis for a Bioinformatics and Computational Genomics laboratory which focuses on high-throughput…

I’m working with paired-end wgs data I downloaded from TCGA. I’m trying to extract the reads that align to a specific region, extract only those reads to two fastq files, one for each pair. Unfortunately, I am getting a different number of reads in both fastq files because some of…

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…

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…

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…

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…

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…

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…

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…

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,…

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…

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…

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…

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…

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…

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…

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…

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…

 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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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,…

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…

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:…

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…

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…

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……

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…

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…

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:…

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…

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…

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….

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…

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…

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…

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,…

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 ||…

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…

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…

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…

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…

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….

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,…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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)…

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…

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…

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)….

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…

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…

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…

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…

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…

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…

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….

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…

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…

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…

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…

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…

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…

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…