Tag: PacBio

The Biostar Herald for Monday, February 06, 2023

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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Spatial and NGS Dominate Proceedings at AGBT 2022

Attending the Advances in Genome Biology and Technology (AGBT) meeting in June 2022 in Orlando, FL, was like drinking from a firehose of genomic information. Or rather, two firehoses. The first let loose a steady stream of information about progress in spatial biology. Speakers shared their excitement over new discoveries,…

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All of Us Researchers Make Case for Long Reads in Population Sequencing

NEW YORK – Researchers associated with the National Institutes of Health’s All of Us research project are calling for the increased use of long-read sequencing technologies in this and other population-scale sequencing efforts. Even using the technologies available three years ago, the authors of a pilot study posted to BioRxiv…

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New Long Amplicon Analysis Tool Analyzes Single Molecule Real-Time Sequencing (SMRT) Data

Press Release Summary: Generates highly accurate, phased and full-length consensus sequences for multiple genes in a single sequencing run Provides complete, uniform and unbiased coverage across long amplicons Applications include full-length 16S, 18S and ITS rRNA gene sequencing Original Press Release: CD Genomics Introduces Professional and Mature Long Amplicon Analysis…

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Next Generation Sequencing (NGS) Market Growth Opportunities and Competitive Scenario 2032

Next Generation Sequencing (NGS) Market: Analysis and Insights Next Generation Sequencing (NGS) Market report provides details of market share, new developments and product pipeline analysis, the impact of domestic and localized market players, analyses opportunities in terms of emerging revenue pockets, changes in market regulations, product approvals, strategic decisions, product…

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Cost-effective and accurate genomics analysis with Sentieon on AWS

This blog post was contributed by Don Freed, Senior Bioinformatics Scientist, and Brendan Gallagher, Head of Business Development at Sentieon; and Olivia Choudhury, PhD, Senior Partner Solutions Architect, Sujaya Srinivasan, Genomics Solutions Architect, and Aniket Deshpande, Senior Specialist, HPC HCLS at AWS. The year 2022 was an exciting one for genomics…

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The $100 genome: What breaking this accessibility barrier means for the future of genetic testing

Cheaper sequencing will also aid researchers working on diseases which have traditionally been underfunded. Bamshad cites cystic fibrosis, a condition which affects around 40,000 children and adults in the U.S., as one particularly pertinent example. “Funds for gene discovery for rare diseases are very limited,” he says. “We’re one of…

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Next Generation Sequencing Market Business Strategies,

Next Generation Sequencing Market The Business Research Company’s global market reports are now updated with the latest market sizing information for the year 2023 and forecasted to 2032 As per the next-generation sequencing market report by The Business Research Company, the growing number of cases with chronic conditions such as…

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PacBio hiring Scientist II, Field Applications Bioinformatics Support in Georgia

PacBio’s single molecule, real-time DNA sequencing platforms are transforming the future of medicine, basic science, and agriculture. Our mission is to transform the way humankind acquires, processes, and interprets data from living systems through innovative tools for biological research. To extend our team, we are looking for a bioinformatics field…

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A chromosome-level genome assembly of Plantago ovata

Genome assembly and chromosome identification A Plantago ovata genome reference was generated by utilizing a total of 5.98 M (7 cells, 40.21 Gb, N50 = 10.45 Kb, 50 bp–121.17 Kb) PacBio long reads and 636.5 million (47.74 Gb) Hi-C short-reads. PacBio reads were used to assemble contigs, while Hi-C reads were used to achieve chromosome-level assembly. The final…

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The Promise of Large Language Models in Genomics

Contributed Commentary by Vanessa Braunstein, NVIDIA  January 27, 2023 | Elucidating information directly from DNA to understand RNA’s and human proteins’ downstream structure and function is the holy grail of nearly a century of molecular biology research. The central dogma of the field—that DNA is transcribed into RNA before translation…

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five areas set to be transformed in 2023 –

2022 was a banner year for genomics. In March, the collaborative T2T consortium published the first complete telomere-to-telomere sequence of the human genome, filling in the last 8% of the 3 billion base pairs that make up our DNA. And in the UK specifically, genomics remained high on the national…

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Plant / Animal Whole Genome PacBio SMRT Sequencing | Life Science & Biotechnology Laboratory Singapore

Plant / Animal Whole Genome PacBio SMRT Sequencing Bio Basic Asia Pacific is providing PacBio SMRT sequencing for animal/plant whole genome sequencing to build better genomes and lead to the breakthrough discovery. PacBio denovo genome assemblies deliver megabase-Size contig N50s, consensus accuracies above 99.99%, and phased haplotypes so scientists can do more…

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Research Assistant (Bioinformatics Support) at Nanyang Technological University Singapore

Job Description The Singapore Centre for Environmental Life Sciences Engineering (SCELSE) invites applications for the position of Research Assistant.  The Singapore Centre for Environmental Life Sciences Engineering (SCELSE) is a unique interdisciplinary Research Centre of Excellence (RCE), funded by National Research Foundation, Ministry of Education, Nanyang Technological University (NTU) and…

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First Provider in Germany: CeGaT Offers Sequencing Services Based on PacBio’s SMRT Technology

Disclaimer: You are now leaving PharmiWeb.com website and are going to a website that is not operated by us. We are not responsible for the content or availability of linked sites. ABOUT THIRD PARTY LINKS ON OUR SITE PharmiWeb.com offers links to other third party websites that may be of…

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Pacific Biosciences of California, Inc. Announces Proposed Public Offering of Common Stock

MENLO PARK, Calif., Jan. 24, 2023 /PRNewswire/ — Pacific Biosciences of California, Inc. (Nasdaq: PACB) (“PacBio”) today announced that it intends to offer and sell $150.0 million of shares of its common stock in an underwritten public offering. PacBio also intends to grant the underwriters a 30-day option to purchase…

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Pacific Biosciences of California, Inc. Announces Pricing of Upsized Public Offering of Common Stock

MENLO PARK, Calif., Jan. 24, 2023 /PRNewswire/ — Pacific Biosciences of California, Inc. (Nasdaq: PACB) (“PacBio”) today announced that it has priced its previously announced underwritten public offering of 17,500,000 shares of its common stock at a price to the public of $10.00 per share. PacBio has granted the underwriters…

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Genomic analysis of an ultrasmall freshwater green alga, Medakamo hakoo

Materials Medakamo hakoo 311 was obtained from the personal aquarium of Prof. Kuroiwa (Kagurazaka, Tokyo, Japan)4. The M. hakoo strain was cultured in 0.05% HYPONeX (HYPONeX Japan Corp., Ltd., Osaka, Japan) liquid medium and on 0.05% HYPONeX gellan gum-based solid medium in plates. Cyanidioschyzon merolae 10D (Toda et al. 1995)…

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Esox Biologics hiring Head of Bioinformatics in London, England, United Kingdom

Esox Biologics is curating the UK’s most comprehensive aquatic pathogen database. Our next-generation sequencing platform is revealing the total microbial landscape across aquatic farms by genotyping the unculturable majority of microorganisms through de novo whole-genome sequencing. You will join a team that works alongside farmers, veterinarians and government bodies, to assist in the…

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Tuberculosis Pathogen Dynamics, Drug Susceptibility Detected With Nanopore Sequencing

Investigators at the European Bioinformatics Institute’s European Molecular Biology Laboratory and elsewhere consider the feasibility of Oxford Nanopore long-read sequencing to study the spread and drug susceptibility of tuberculosis-causing Mycobacterium tuberculosis pathogens. As they report in The Lancet Microbe, the researchers set the SNP clusters and drug sensitivity predictions found…

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Alternative splicing and genetic variation of mhc-e: implications for rhesus cytomegalovirus-based vaccines

The gene expression of Mamu-E is regulated by extensive alternative splicing that is conserved among HLA-E isoforms To accurately define Mamu-E transcript structures, we aimed to use high-quality, full-length transcript sequences obtained by long-read transcriptome sequencing41. Since the sequences of MHC genes are very similar, it was critical that we…

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Research Asst., (Bioinformatics Support) [R00005704] at Nanyang Technological University Singapore

Job Description The Singapore Centre for Environmental Life Sciences Engineering (SCELSE) is a unique interdisciplinary Research Centre of Excellence (RCE), funded by National Research Foundation, Ministry of Education, Nanyang Technological University (NTU) and National University of Singapore (NUS). Hosted by NTU in partnership with NUS, SCELSE is linking new insights…

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Bioinformatics Software Engineer at eGenesis

COMPANY MISSION At eGenesis, we aspire to deliver safe and effective human transplantable cells, tissue and organs utilizing the latest advancements in genome editing.  POSITION SUMMARY We are seeking a skilled Bioinformatics software engineer to join our thriving computational biology team. In this role, you will lead development of reproducible…

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VIB hiring Postdoc Position in Bioinformatics, Metagenomics and the Human Microbiome in Leuven, Flemish Region, Belgium

The lab of Jeroen Raes (VIB, KU Leuven) is looking for a postdoctoral researcher in the computational analysis of microbiome data, with a particular emphasis on human-associated microbial communities in health and disease.Projects Will Focus On(i) bioinformatics/statistics method development for joint host and microbiota data analysis, multi-omics and clinical data…

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Bioinformatics Analyst Jobs

We have an exciting contract opportunity for a Bioinformatics analyst to support a collaboration between the Biologics Science and Technology group and Genomics Research Center, in which we are using genomics tools to optimize the development of better Chinese Hamster Ovary (CHO) cells for biologics manufacturing. The ideal candidate will…

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Bioinformatics Analyst II (Remote) Position In North Chicago, IL

Job Description To discuss more about this job opportunity, please reach out to Chitrank Rastogi (LinkedIn URL – www.linkedin.com/in/chitrank-rastogi-55119a102/), email your updated resume at chitrank.rastogi@collabera.com or give me a call at (425) 523-1648. Thank you! Job Description:Job Roles & Responsibilities: We have an exciting contract opportunity for a Bioinformatics analyst…

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Bioinformatics Analyst-Entry Level Position In North Chicago, IL

Description du poste Bioinformatics Analyst Supports a collaboration between the Biologics Science and Technology group and Genomics Research Center, in which we are using genomics tools to optimize the development of better Chinese Hamster Ovary (CHO) cells for biologics manufacturing. The ideal candidate will have broad experience in genomics data…

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Gene fusion detection and characterization in long-read cancer transcriptome sequencing data with FusionSeeker | Cancer Research

Gene fusions are prevalent in a wide array of cancer types with different frequencies. Long-read transcriptome sequencing technologies, such as PacBio, Iso-Seq, and Nanopore direct RNA sequencing, provide full-length transcript sequencing reads, which could facilitate detection of gene fusions. In this work, we developed a method, FusionSeeker, to comprehensively characterize…

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Genomic signatures associated with maintenance of genome stability and venom turnover in two parasitoid wasps

Genomic features of two Anastatus wasps, A. japonicus and A. fulloi We employed PacBio high-fidelity (HiFi) long-read sequencing and Illumina short-read sequencing technologies to generate high-quality contigs for two Anastatus wasps, A. japonicus and A. fulloi (Supplementary Tables 1 and 2). These contigs were further scaffolded using Hi-C libraries to…

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Next Generation Sequencing (NGS) Market, Outlook Size Share Industry Segmentation, Targeting, Positioning Exclusive Report by |Quince Market Insights

Next Generation Sequencing (NGS) Market Scope The Next Generation Sequencing (NGS)-market size was assessed at USD in 2023. Developing number of organizations tapping the nearness Next Generation Sequencing (NGS) market, alongside expanding interests in the Next Generation Sequencing (NGS) Market innovation, is supposed to move the business development. expected to…

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Order of reads in Long read FASTQ file

Order of reads in Long read FASTQ file 0 Hi all, FASTQ files contain sequencing reads ‘as they come off the sequencing instrument.’ Is there any particular order to them in long read fastq file for ONT and PacBio? E.g. based on the position of the flow cell? Quality? I…

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Run fastqc reports for each of the fastq files in:

Run fastqc reports for each of the fastq files in: /data/CompRes/seq_platform_data/ To run the fastqc reports, you can write a script that will execute the following command (edited for you) for each file: fastqc /data/CompRes/seq_platform_data/<inputfastq> -o /home/ASURITE/BIO439/module4/ Then transfer the html files to your local computer and view them, so…

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MicrobioSeq Boosts Microbial Community Research with Long-Read Metagenomic Sequencing

MicrobioSeq represents the microbial genomics division of CD Genomics, headquartered in New York, USA. CD Genomics is a genomics service company with a good reputation for providing reliable sequencing, genotyping, microarray, and bioinformatics services. The company provides the long-read metagenomics sequencing service using PacBio SMRT platform, which can sequence multiple…

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Research Fellow, School of Medicine, Dentistry & Biomedical Sciences job with QUEENS UNIVERSITY BELFAST

Job description The School of Medicine, Dentistry & Biomedical Sciences (MDBS) at Queen’s University Belfast, is currently seeking to appoint an exceptional candidate to the post of Research Fellow. The successful candidate will provide genomics support for the QUB SARS-CoV-2 sequencing team, which was created to deliver large-scale and rapid…

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PacBio SMRT VS Nanopore Sequencing, battle of the long reads : bioinformatics

Honestly, it very much depends on what you want to do/get out of the sequencing. Nanopore seems more flexible in some aspects, but I would generally work together with sequencing facilities and discuss your project with them. Normally, they have a good feeling for which technology might be best for…

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Careers in genomics – The Hindu

As scientists and other professionals use discoveries in genetics to revolutionise the world, careers in genetics and genomics are booming, given the advances in the field of personalised medicine, DNA sequencing technologies and commercial applications of genetics research. ‘Genomics’ stands for the study of whole genomes. While ‘genes’ are instructions…

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NHLS Vacancies for Nurses – Bioinformatics Scientist

vacancieshutem 2 mins ago Job Responsibilities: Engage with NICD users and assist with next-generation sequencing (NGS) data analysis .Perform basic and advanced analysis and interpretation on data produced from next generation sequencing systems (e.g. Illumina, PacBio or Ion torrent platforms) as well as…

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Low exonic mapping of RNASeq data to draft genome. Should I suspect poor annotation?

Low exonic mapping of RNASeq data to draft genome. Should I suspect poor annotation? 0 I am working on RNASeq data for DE from a non-traditional organism (Artemia franciscana, a eukaryotic arthropod) whose draft genome was published last year. I should note here that although the genome was assembled with…

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Rsubread featurecounts

Rsubread featurecounts 1 Hi there, I seem to be getting this error when reading in a BAM file which was generated by PBMM2 align on pacbio data. I have tried to google the error message but there are no results. I wonder if anyone has ideas on what the error…

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Lh3 Minimap2 Issues

Issue Title State Comments Created Date Updated Date Mapping reads against multi references. Any proposition? open 0 2022-06-28 2022-06-30 Inversion between tandem repeats yields misalignment closed 1 2022-06-21 2022-06-30 use minimap2 to extract mitochondrial reads from genome assembly open 0 2022-06-20 2022-06-30 Asking for #301 to be reopened closed 0…

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what is rnaseq – Ques Answer

rnaseq CD Genomics has been providing the accurate and affordable RNA-Seq (RNA sequencing) service for decades. We combine both Illumina (short reads) and PacBio (long reads) platforms to obtain the transcriptome that allows de novo assembly or re-sequencing for bacteria, plants, animals and humans. rnaseq CD Genomics has been providing…

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MicrobioSeq Releases Nanopore-Based Microbial Epigenomics Solutions to Accelerate Your Research

MicrobioSeq is the microbial genomics division of CD Genomics, committed to delivering comprehensive microbial solutions to human health, agriculture, the environment, and industry by characterizing microbiomes and leveraging microorganisms. The company recently announced the launch of Nanopore-Based Microbial Epigenomics Solutions to detect more types of DNA modifications.   Epigenetic modifications…

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In vivo hypermutation and continuous evolution

Arnold, F. H. Design by directed evolution. Acc. Chem. Res. 31, 125–131 (1998). Google Scholar  Packer, M. S. & Liu, D. R. Methods for the directed evolution of proteins. Nat. Rev. Genet. 16, 379–394 (2015). Google Scholar  Drake, J. W., Charlesworth, B., Charlesworth, D. & Crow, J. F. Rates of…

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DataSheet1_Enhancing Long-Read-Based Strain-Aware Metagenome Assembly.PDF

Microbial communities are usually highly diverse and often involve multiple strains from the participating species due to the rapid evolution of microorganisms. In such a complex microecosystem, different strains may show different biological functions. While reconstruction of individual genomes at the strain level is vital for accurately deciphering the composition…

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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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Mitogenome-wise codon usage pattern from comparative analysis of the first mitogenome of Blepharipa sp. (Muga uzifly) with other Oestroid flies

Outcome of DNA sequencing, assembly, and validation In this study, initially total DNA was isolated from the finely chopped, full-grown pupa of Blepharipa sp. The NanoDrop spectrophotometer (1294 ng/μl) and the Qubit fluorometer (732.8 ng/μl) both found that the concentration of total DNA in the sample at an optimum level for mitochondrial DNA enrichment. The Tape Station profile showed…

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different result using minimap2 and pbmm2

Hi all! I am analysing CSS Pacbio data and each sample came from different run, in particular I have three files for each sample. I tested both pbmm2 and minimap2 to align my long reads, after getting the consensus sequences. This is the command I used to run mnimap2: minimap2…

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Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes

Sequencing data We used publicly available sequencing data from the GIAB consortium45, 1000 Genomes Project high-coverage data46 and Human Genome Structural Variation Consortium (HGSVC)4. All datasets include only samples consented for public dissemination of the full genomes. Statistics and reproducibility For generating the assemblies, we used all 14 samples for…

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Pacific Biosciences, Corteva Agriscience Collaborate on High-Throughput Sequencing

NEW YORK – Pacific Biosciences said on Monday that it is collaborating with Corteva Agriscience to develop custom workflows for plant, pest, and microbial sequencing. Under the terms of the project, the partners will establish high-throughput workflows for DNA extraction and library preparation to enable sequencing of thousands of samples….

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At ABRF Meeting, T2T Consortium Describes Improvements of Complete Human Genome

PALM SPRINGS, Calif. — Researchers from the Telomere-to-Telomere (T2T) Consortium have generated an assembly of a complete human reference genome that could lead to better variant calling in the clinic and inform new studies of cell biology. The results of the project were presented by Karen Miga, an investigator at…

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Scientists sequence the most complete human genome yet

A team of almost 100 scientists part of the Telomere-to-Telomere (T2T) Consortium has successfully sequenced the most complete human genome yet. If you’re thinking “Wait a minute — didn’t scientists produce the complete human genome sequence almost two decades ago?” Well, you wouldn’t be wrong. The Human Genome Project finished…

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Single-cell Iso-Sequencing enables rapid genome annotation for scRNAseq analysis

. 2022 Mar 3;220(3):iyac017. doi: 10.1093/genetics/iyac017. Affiliations Expand Affiliations 1 Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA. 2 Presidential Initiative in Data Science, University of Oregon, Eugene, OR 97403, USA. Item in Clipboard Hope M Healey et al. Genetics. 2022. Show details Display options Display options…

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CEFAS22-11 Next Generation Sequencing Services Framework: | Construction Tenders

Tender Details Reference ocds-h6vhtk-031eee Common Procurement Vocabulary Technical analysis or consultancy services Procurement Method Open procedure Value £500,000 Tender Details Reference ocds-h6vhtk-031eee Common Procurement Vocabulary Technical analysis or consultancy services Procurement Method Open procedure Value £500,000 Section I: Contracting authority I.1) Name and addresses CEFAS Pakefield Road Lowestoft NR33 0HT…

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Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics | Environmental Microbiome

Steen AD, Crits-Christoph A, Carini P, DeAngelis KM, Fierer N, Lloyd KG, Cameron TJ. High proportions of bacteria and archaea across most biomes remain uncultured. ISME J. 2019;13:3126–30. PubMed  PubMed Central  Google Scholar  Goh KM, Shahar S, Chan K-G, Chong CS, Amran SI, Sani MH, Zakaria II, Kahar UM. Current…

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UMD Genome group

An email was successfully sent. MaSuRCA assembler MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454, Pacbio and…

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Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis

INTRODUCTION Next-generation sequencing (NGS) has revolutionized many areas of biological research (1, 2), providing ever-more data at an ever-decreasing cost. One such area is microbiome research, the study of microbes in their theater of activity using metagenomic sequencing (3). Here, deep short-read sequencing, and improving performance of long-read sequencing, are…

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Hinted by Clinical Misclassification of a Neisseria mucosa Strain

The taxonomy of the genus Neisseria remains confusing, particularly regarding Neisseria mucosa and Neisseria sicca. In 2012, ribosomal multi-locus sequence typing reclassified both as N. mucosa, but data concerning 17 N. sicca strains remain available in GenBank. The continuous progress of high-throughput sequencing has facilitated ready accessibility of whole-genome data,…

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Find Transposon Element insertions using long reads (nanopore), by alignment directly. (minimap2)

find_te_ins is designed to find Transposon Element (TE) insertions using long reads (nanopore), by alignment directly. (minimap2) Install $ git clone github.com/bakerwm/find_te_ins.git&#13; $ cd find_te_ins Change the following variables upon your condition: genome_fa and te_fa in line-10 and line-11; $ bash run_pipe.sh run_pipe.sh Prerequisite minimap2 – 2.17-r974-dirty, align long…

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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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An intronic transposon insertion associates with a trans-species color polymorphism in Midas cichlid fishes

Conflicting results suggest a missing variant In order to narrow down candidates for the causal genetic variant, we performed genome-wide association mapping separately in individual lake populations (previously, association mapping was only performed across the whole species flock5). Interestingly, despite clear association peaks in the crater lakes (Fig. 1a, b), the…

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Insight into the symbiotic lifestyle of DPANN archaea revealed by cultivation and genome analyses

Significance The DPANN superphylum is a grouping of symbiotic microorganisms categorized based on their genomic contents and a few examples of cultivation experiments. Although the genome information of DPANN archaea is increasing year by year, most of them have remained uncultivated, limiting our knowledge of these organisms. Herein, a thermoacidophilic…

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CRISPR-Cas12a ribonucleoprotein-mediated gene editing in the plant pathogenic fungus Magnaporthe oryzae

. 2021 Dec 24;3(1):101072. doi: 10.1016/j.xpro.2021.101072. eCollection 2022 Mar 18. Affiliations Expand Affiliation 1 Department of Plant Pathology, Kansas State University, Manhattan, KS, USA. Free PMC article Item in Clipboard Jun Huang et al. STAR Protoc. 2021. Free PMC article Show details Display options Display options Format AbstractPubMedPMID . 2021 Dec…

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Using Minimap2 with FMLRC2

Using Minimap2 with FMLRC2 1 Hello all, I am using FMLRC2 (github.com/HudsonAlpha/rust-fmlrc) to correct PacBio reads with Illumina reads for hybrid genome assembly. Since FMLRC2 only corrects reads (does not do any assembly) another program is needed. In the paper published on FMLRC minimap (now succeeded by minimap2, github.com/lh3/minimap2) was…

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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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An error about using DADA2 in QIIME2 – Community Plugin Support

Hi everyone,I analyzed my pacbio data according to this PR, but an error was happened: Error in h(simpleError(msg, call)) : Error: invalid class “SRFilterResult” object: superclass “Mnumeric” no t defined in the environment of the object’s class stop Traceback (most recent call last): File “/home/xxx/miniconda3/envs/qiime2-2021.4/lib/python3.8/site- packages/q2_dada2/_denoise.py”, line 361, in denoise_ccs…

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NIH-SOAR-NCI-Bioinformatics Scientist in Rockville, MD

Axle Informatics is a bioscience and information technology company that offers advancements in translational research, biomedical informatics, and data science applications to research centers and healthcare organizations around the globe. With experts in biomedical science, software engineering, and program management, we focus on developing and applying research tools and techniques…

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A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches

BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy while reducing the memory space usage of two important applications: 1) finding overlapping reads and 2) read mapping. Finding fuzzy seed matches enable BLEND to find both 1) exact-matching seeds…

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PacBio hiring Senior Bioinformatics Scientist, Primary Analysis in San Diego, California, United States

Please be aware that, as a condition of employment, proof of COVID vaccination is required for all U.S.-based employees (subject to limited exceptions).Title: Bioinformatics Scientist Location: San Diego, CA, or Menlo Park, CA , or Remote Position Summary An emerging leader in next-generation sequencing technology is seeking a driven Bioinformatics…

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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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High-throughput sequencing of 16S rRNA gene analysis reveals novel taxonomic diversity among vaginal microbiota in healthy and affected sows with endometritis

Available online 7 December 2021 doi.org/10.1016/j.rvsc.2021.12.003Get rights and content Highlights • Corynebacterium_1, Clostridium_sensu_stricto_1, Porphyromonas, Anaerococcus, Streptococcus, and Bacteroides were the core microbiota in all healthy sows. • V3-V4 region of the 16S rRNA gene sequence and full-length 16S rRNA analysis confirmed that Burkholderia was a dominant genus in endometritis sows…

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rRNA Analysis Based on Long-Read High-Throughput Sequencing Reveals a More Accurate Diagnostic for the Bacterial Infection of Ascites

. 2021 Nov 17;2021:6287280. doi: 10.1155/2021/6287280. eCollection 2021. Affiliations Expand Affiliations 1 Department of Infectious Diseases, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China. 2 Institute of Applied Genomics, Fuzhou University, Fuzhou 350108, China. Item in Clipboard Xiaoling Yu et al. Biomed Res Int. 2021. Show details Display options…

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Toward a genome sequence for every animal: Where are we now?

Abstract In less than 25 y, the field of animal genome science has transformed from a discipline seeking its first glimpses into genome sequences across the Tree of Life to a global enterprise with ambitions to sequence genomes for all of Earth’s eukaryotic diversity [H. A. Lewin et al., Proc. Natl….

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In Conversation with Christian Henry, CEO, PacBio

Christian Henry, CEO, PacBio It’s fair to say long-read sequencing company PacBio has been through some trials in the past few years, not the least of which was the scuttled merger it had planned with short-read sequencing behemoth Illumina. But since that time, the company has revamped its leadership team…

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Postdoc position in Bioinformatics – Comparative Genomics

Description Posted Date 18 Nov 2021 Locations Leuven Center VIB KU Leuven Center for Microbiology Type Post doctoral Positions 1 About the Lab The lab for Systems Biology of Kevin Verstrepen is a research team at VIB & University of Leuven. Our team focuses on genomics, genetics, epigenetics, transcriptomic, and…

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Purge duplicates from hifiasm assembly v1.0 (HiFi genome assembly stage 3)

0 HiFiASM 1o assembly Primary assembly input from hifiasm workflow, in FASTA format. 1 HiFi reads as FASTQ Raw HiFi reads input, in FASTQ format. 2 Step 1. Base-level coverage toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy3 3 Step 1. Run minimap2 to align pacbio data and generate paf files, toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.20+galaxy2 4 Step 1. Split an…

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Bioinformatics NGS Data Analyst position in Andover, Massachusetts

Job Description: Position Summary: The qualified candidate will join the Analytical Research and Development Microbiology and Strategy Testing organization in Andover, MA, a QC (GMP) laboratory that supports biotherapeutic clinical manufacturing. Candidate will report directly to Microbiology Group Leader (Principal Scientist, Ph.D.). We are recruiting an expert…

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Human Genome and DNA Sequencing

Author: Brianna Nee Editor: Liane Xu and Megan Liu Artist: Tiffany Gao The human genome consists of about 3.2 billion base pairs, which make up approximately 30,000 genes. When genes are expressed, the sequence of bases is transcribed in the nucleus from DNA into RNA. Then, in the ribosome, the…

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Biopython download nucleotide records without sequences (or skip huge sequences)

I am trying to download information from NCBI Entrez databases (nucleotide), using Biopython package. I don’t need molecular data at all. I just want to check the textual information about certain records, to see references, authors, journals, and information about voucher specimens from which the genome sample was extracted. My…

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Top Nucleic Acid Sequencing Startups

Last Updated: November 13, 2021 Business models evolve with time, sometimes due to changes in the market and sometimes due to advent of technology, resulting in emergence of new exciting trends. We at Tracxn closely track the startup ecosystem from across the world and we have come across a whole…

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Genome of the estuarine oyster provides insights into climate impact and adaptive plasticity

1. Hoegh-Guldberg, O. & Bruno, J. F. The impact of climate change on the world’s marine ecosystems. Science 328, 1523–1528 (2010). CAS  PubMed  Google Scholar  2. Chou, C. et al. Increase in the range between wet and dry season precipitation. Nat. Geosci. 6, 263–267 (2013). CAS  Google Scholar  3. Li,…

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Nature Papers Present Chromatin Analysis Approach, Gene Targets to Improve Bread Wheat, More

A computational framework for analyzing single-cell chromatin data is presented in Nature Methods this week. Called Signac, the resource enables end-to-end analysis of chromatin data and includes functionality for a range of analysis tasks including identifying cells from background non-cell-containing barcodes, calling peaks, quantifying counts in genomic regions, and quality…

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Annotation with egg-mapper

Annotation with egg-mapper 0 Hello everyone, I have assembled a bacterial genome from PacBio reads. I would like know annotate that genome. I used egg-mapper to do that. Prodigal detects 4131 CDS and egg-mapper outputs an GFF annotation file. Is there a way to filter that GFF, in order to…

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Samtools Samtools Statistics & Issues

  Issue TitleStateCommentsCreated DateUpdated DateClosed Datesamtools 1.10 csi vs 1.13 generation/reading closed 22021-11-012021-10-272021-11-03mpileup: –output-BP-5 switches output column 7 and 8 open 22021-11-012021-10-27-ampliconclip bug when hardclipping odd-length sequences from the left closed 12021-10-232021-10-272021-11-03Feature Request: Flag in ampliconclip to clip out everything except target sequence open 22021-10-222021-10-27-samtools markdup slow in docker open…

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What is the range that Solexa quality scores can take?

The encoding is compatible with a P – PacBio Phred+33, HiFi reads typically (0, 93) See the Wikipedia page that GenoMax also linked. Though the sequencing run is from 2010 and is not on PacBio I think what happened is that the upper limit was not truncated to 40 as…

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A complete sequence of mitochondrial genome of Neolamarckia cadamba and its use for systematic analysis

Assembly of mitochondrial genome MtDNA sequence of N. cadamba was determined using PacBio sequencing technique and was successfully assembled in two genome circles. This probably reflects the feature of rapid evolution of structure of plant mitochondrial genomes38,39,40. Figure 1 shows two parts of circular structure of the mitochondrial genome, designated as…

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Counting hexamers in fasta sequence and identify its structure (and interruptions)

I have a lot of fasta files, each one with thousand of reads containing the hexameric motif “CCCTCT”. The hexameric motif is highly continuous in most cases but interruptions may occur. I need to count the hexameric motif keeping the read ID and identify their structure (CCCTCT)n. These interruptions are…

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The Biostar Herald for Monday, November 01, 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 Mensur Dlakic, Istvan Albert, GenoMax, and was…

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Run purge_dups with PacBio hifi reads and HiCanu assembly

Run purge_dups with PacBio hifi reads and HiCanu assembly 0 Hi there, I was wondering if it is possible to run purge_dups on a de novo genome assembly generated with HiCanu and PacBio hifi reads without any short reads. One of the arguments in step 1 of the “usage” section…

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failed to write header to “-“

[bam_sort_core] merging from 32 files and 16 in-memory blocks… samtools sort: failed to write header to “-“ 0 Hi, When I run script samtools sort -@ 16 -T “path/to/temp” “$bamfile” > “$_sorted.bam, I get this error message: [bam_sort_core] merging from 112 files and 16 in-memory blocks… samtools sort: failed to…

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Run purge_dups with PacBio hifi reads and HiCanu aassembly

Run purge_dups with PacBio hifi reads and HiCanu aassembly 0 Hi there, I was wondering if it is possible to run purge_dups on a de novo genome assembly generated with HiCanu and PacBio hifi reads without any short reads. One of the arguments in step 1 of the “usage” section…

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Platanus-allee phasing fail: Error(13): Error, SolveDBG exception!!

Platanus-allee phasing fail: Error(13): Error, SolveDBG exception!! 0 Hello there, I am using Platanus-allee 2.2.2 to generate hybrid assembly of Illumina short reads and PacBio reads. I have got contigs.fa from short reads but phasing step with PacBio reads gives the following error after running for couple of hours Error(13):…

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Pacific Biosciences hiring Staff Scientist, DNA Sequencing Sample Prep in Menlo Park, California, United States

Pacific Biosciences seeks a Senior/Staff/Principal Scientist with a strong molecular biology background to join the sample prep team. This position will contribute to development of the up-front DNA preparation for Pacific Biosciences SMRT™ sequencing platform, as well as support of internal research efforts, by working with a team that is…

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A rapidly reversible mutation generates subclonal genetic diversity and unstable drug resistance

Different mechanisms of adaptation have different timescales. Epigenetic changes are often rapid and reversible, while most genetic changes have nearly negligible rates of reversion (1). This poses a challenge for genetic adaptation to transient conditions such as drug treatment; mutations that confer drug resistance are often deleterious in the absence…

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CMA Chief exec: Crack downs on tech monopolies will safeguard London’s competitive edge

Effective competition is the lifeblood of a thriving economy. The chance to succeed with hard work and a good idea is a source of hope, and opportunity to entrepreneurs everywhere. While monopolies stifle innovation and focus on protecting their existing profits, competition leads to vibrancy and new ideas. Ensuring digital…

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Cereal Bioinformatics Specialist at The James Hutton Institute

The Vacancy This is a three-year ‘tenure track’ post: in the third year, if there is a business case and the candidate meets relevant academic criteria, the contract will be made indefinite. The work undertaken by The James Hutton Group is right at the top of the global agenda tackling…

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analysing basemods in old pacbio data; advice on setting up SMRT link/tools

analysing basemods in old pacbio data; advice on setting up SMRT link/tools 0 I have pacbio data from old sequencing projects and I want to analyse them for base modifications and motifs but I no longer have access to a SMRT link setup at a sequencing facility. I would need…

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QC metrics from pacbio long reads data

QC metrics from pacbio long reads data 0 Hello, I have two samples that were sequenced using pacbio technology. These samples are different in terms of their shearing methods. I also have SMRTLink installed through command line interface. I want to run some primary analysis to compare these samples, for…

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how to map Pacbio CCS fastq

how to map Pacbio CCS fastq 1 I have a Pacbio CCS fastq like this I want to map to genome, and this is my command and out. I want to know how to solve it. Is this fastq correct? Thanks minimap2 Pacbio • 25 views It might pay to…

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mapping long-reads to a reference library

mapping long-reads to a reference library 1 Hi, I have long, pacbio, reads and I have a reference library of only repeats, I want to map the long reads on the repeats library using bwa mem, is this command correct? bwa index mmm.pacbio.fastq.gz bwa mem mmm.pacbio.fastq.gz repeat-library.fasta | samtools sort…

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Reimagining DNA Sequencing With Long Reads: Christian Henry on The Long Run

Today’s guest on The Long Run is Christian Henry. Christian is the CEO of Menlo Park, Calif.-based PacBio. It makes DNA sequencing instruments that are used by scientists around the world. Christian Henry, CEO, PacBio The company has long toiled in the shadow of the market leader – some would…

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