Category: PacBio

The Biostar Herald for Monday, November 08, 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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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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Job: Principal Investigator – Bioinformatics

Education and Experience : – PhD with at least 5 years industrial/academic experience in bioinformatic and computational analysis of biological systems. – Experience in programming particularly Linux, Python, Java or R, to provide analytical tools for querying large sequence and relational databases. Familiarity with HP cluster computing in this context…

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sam2tsv listing incorrect reference sequence & positions

Duplicate of: github.com/lindenb/jvarkit/issues/190 Hi can anyone help me resolve the issue I’m having with sam2tsv. It is a nifty piece of software but I have been encountering issues with it regarding the numbering of nucleotides it shows for the reference sequence. Here’s what sam2tsv tells me: The nucleotide string marked…

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A Tool for Rapid Sequence Comparison

MinHash Sketch is a method of rapidly comparing large strings or sets. In genomics, you can use it like this: 1) Gather all the kmers in a genome. 2) Apply a hash function to them. 3) Keep the 10000 smallest hashcodes and call this set a “sketch”. If you do…

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Keeping up with the human genome

The human genome is made up of over three billion base pairs of DNA, which in turn create the 23 chromosome pairs which make up a human being’s genetic code. The initial draft sequence of the human genome was unveiled by Celera Genomics and the International Human Genome Sequencing Consortium…

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Genome Assembly and Annotation

News:Genome Assembly and Annotation 0 Dear all, registrations are now open for the Physalia course on “Genome Assembly and Annotation”: www.physalia-courses.org/courses-workshops/course20/ When: March, 14th-18th This course will introduce biologists and bioinformaticians to the concepts of de novo assembly and annotation, providing a theoretical framework and practical examples. A variety of…

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Manager, Bioinformatics Shared Resource – jobRxiv

The Cold Spring Harbor Laboratory Cancer Center is looking for a highly motivated Senior Computational Biologist to lead the Bioinformatics Core of the Sequencing Technologies and Analysis Shared Resource, which develops new technologies at the cutting edge of genome science, including new assays that take advantage of long-read and single-cell…

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Single cell RNA sequencing (scRNA-seq) in cardiac tissue

Introduction Cardiovascular diseases (CVDs) are the leading cause of death globally, taking an estimated 17.9 million (32.1%) lives in 2015, up from 12.3 million (25.8%) in 1990.1,2 CVDs are highly heterogeneous diseases involving a group of disorders of the heart and blood vessels, which include cardiomyopathy, hypertensive heart disease, heart…

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Chromosome-level genome assemblies of five Prunus species and genome-wide association studies for key agronomic traits in peach

Genome assembly In this study, we de novo assembled the plum, Prunus mira, and Prunus davidiana genomes for the first time and improved the peach and apricot genomes by integrating single-molecule real-time (SMRT) long-read sequencing (PacBio), short high-quality Illumina paired-end sequencing, and Hi-C technology. First, we used SMRT reads (99−130 Gb,…

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genbank submission tutorial

These are just a few of the questions answered in this comprehensive overview of Bayesian approaches to phylogenetics. Finally, make sure the Include Primers box is unchecked, as we are not submitting primers with this sequence. Influenza virus sequences. September, 2008. Please download the current version. Some mitochondrial genomes contain CDS’s that…

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PacBio (PACB) Partners with ERGA, Boosts Biodiversity Research

Pacific Biosciences of California, Inc. PACB, also popularly known as PacBio, recently collaborated with The European Reference Genome Atlas (“ERGA”) consortium to aid its efforts with regards to understanding and safeguarding biodiversity. The partnership involves PacBio lending support to biodiversity protection through generation of high-quality reference genomes for European plant…

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genbank submission bankit

Submission of sequence data to NCBI archives . Learn more. This post will show you how to… Careers, General: your contact details, authors, publication, data release date, Original or third-party assembly/annotation, Set designation (if applicable) for multiple sequences of the same locus, Nucleotide sequences in FASTA or alignment format, Source…

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Introduction to DNA Sequencing Technology Part II

Location: 2240 CIEMAS During the past decade, a new generation of high-throughput DNA sequencers has transformed biomedical and biotechnology research. These new technologies have fostered the development of a wide range of applications to basic and clinical research, including SNP discovery, transcriptome profiling, genome sequencing, and epigenetics. The goal of this…

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Global Supply Chain Issues Catch up to Illumina, Leading to Delayed NGS Projects

NEW YORK – Until recently, Illumina had been able to stay ahead of pandemic-related reagent shortages affecting the entire biotech industry. But since the beginning of the summer, customers have noticed that delivery of certain Illumina next-generation sequencing reagents is being delayed by weeks — or even indefinitely. “We are…

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Which files from PacBio output files to use in downstream analysis in R

Which files from PacBio output files to use in downstream analysis in R 0 I just received Pacbio sequences of 16S gene from the core facility. After download, I got 5 files for each sample with following suffix: .ccs.bam longest.bam scraps.bam subreads.bam whitelist From readings, I believe that I should…

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Transposition and duplication of MADS-domain transcription factor genes in annual and perennial Arabis species modulates flowering

Annual and perennial species occur in many plant families. Annual plants and some perennials are monocarpic (flowering once in their life cycle), characterized by a massive flowering and typically produce many seeds before the whole plant senesces. By contrast, most perennials live for many years, show delayed reproduction, and are…

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PacBio’s $600 million Omniome acquisition brings together long and short DNA sequencing

Nearly three years ago, when Pacific Biosciences agreed to be acquired by Illumina, the acquisition was positioned as a pair of companies with complementary DNA sequencing technologies. Antitrust regulators believe that this is not the case, causing these companies to abandon the deal. PacBio now has another deal that aims…

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Submit sequence data to NCBI

Data provision and standards. GEO sequence submission procedures are designed to encourage provision of MINSEQE elements: Thorough descriptions of the biological samples under investigation, and procedures to which they were subjected. Thorough descriptions of the protocols used to generate and process the data. Request updates to accessioned records per the…

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New PacBio Library Prep Method Helps Cover ‘Death Valley’ Between Short and Long Reads

ST. PAUL, MINNESOTA – Researchers from the University of Minnesota have developed a library preparation method for Pacific Bioscience’s Sequel platform that addresses the challenge of sequencing DNA molecules that are too long for short reads but not long enough to make long-read sequencing cost effective. Their solution: link up…

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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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Bioinformatics and Assay Development Scientist II – San Francisco, CA | South San Francisco, CA

Date posted: Sep 16, 2021 Bioinformatics and Assay Development Scientist II – San Francisco, CA The Monogram division of LabCorp, which is focused on high complexity cell-based assay development, has an exciting opportunity for a Scientist to join its R&D Diagnostics Development Team. The selected candidate will design, build and…

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What are the steps of an full lengh RNA seq annotation method?

What are the steps of an full lengh RNA seq annotation method? 0 I have read a few papers, some of them used GenMark, or PacBios proprietary Iso-Seq pipeline but as I’m just a Bachelor’s student I am having trouble understanding how exactly it works. Can some one roughly explain…

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How does PacBio Iso-Seq annotation compare to other pipelines?

How does PacBio Iso-Seq annotation compare to other pipelines? 1 I have no experience in annotation RNA seq data (or genome assembly) but I’ve spent the last weeks ploughing through some papers and looking at manuals. I am wondering why it seems so common that e.g. proprietary pipelines of sequencers…

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The future of ‘next generation’ DNA sequencing | Business

Next Generation Sequencing has been with us for little more than a decade, but has already revolutionised biological science. According to Jonas Korlach, chief scientific officer of US-based sequencing company Pacific Biosciences (PacBio) we are now entering a golden age of sequencing technology and the advanced understanding of genetics it…

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Legacy genetics of Arachis cardenasii in the peanut crop shows the profound benefits of international seed exchange

Significance A great challenge for humanity is feeding its growing population while minimizing ecosystem damage and climate change. Here, we uncover the global benefits arising from the introduction of one wild species accession to peanut-breeding programs decades ago. This work emphasizes the importance of biodiversity to crop improvement: peanut cultivars…

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Whole Genome Sequencing via Pacific Biosciences (PacBio) Sequel DNA Sequencing Systems – 12305B21Q0093, West virginia

This is a combined synopsis/solicitation for commercial items prepared in accordance with the format in subpart 12.6, as supplemented with additional information included in this notice. This announcement constitutes the only solicitation; proposals are being requested and a written solicitation will not be issued.                 (ii) The solicitation number and a…

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Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study

. 2021 Sep;39(9):1129-1140. doi: 10.1038/s41587-021-01049-5. Epub 2021 Sep 9. Jonathan Foox  1   2 , Scott W Tighe  3 , Charles M Nicolet  4 , Justin M Zook  5 , Marta Byrska-Bishop  6 , Wayne E Clarke  6 , Michael M Khayat  7   8 , Medhat Mahmoud  7   8 , Phoebe K Laaguiby  3 , Zachary T…

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Oxford Nanopore Stock: The Internet of Living Things

If you took all the stocks in the world and put them in a single basket, about 58% of that combined market cap would be U.S. stocks. If you want to look that number up, just download a fact sheet for the MSCI ACWI IMI Index. All those cryptic acronyms…

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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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How does PacBio Iso -Seq Annotation compare to other pipelines?

How does PacBio Iso -Seq Annotation compare to other pipelines? 1 I have no experience in annotation or assembly but I’ve spent the last weeks ploughing through some papers and looking at manuals. I am wondering why it seems so common that e.g. proprietary pipelines of sequencers are not used?…

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PacBio sequencing output increased through uniform and directional fivefold concatenation

Strategy and design of the method We sought to develop a simple method to increase the sequencing capability of PacBio CCS to sequence several diverse DNA libraries ~ 870 bp in length that encoded protein variants originating from a directed evolution campaign. To achieve an increase in the throughput of a PacBio sequencing…

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Cancer Mutation Detection Depends on Choices at Each Step of Sequencing, Analysis Pipeline

NEW YORK — An international team of researchers has examined how variations in sequencing approaches can influence the ability to accurately detect cancer mutations, providing guidance for the wider community. The team additionally developed a set of reference samples for benchmarking efforts. Next-generation sequencing approaches are increasingly being adopted to…

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Sudden coverage increase in IGV

Sudden coverage increase in IGV 0 Hello, I was wondering if anyone knows how to interpret this sudden change in coverage in IGV? I’ve aligned illumin reads of the system against the pacbio generated genome. In the vast majority of this genome, the coverage from one base to the next…

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Google Getting Into Genomics? It Already Is

Google parent Alphabet (NASDAQ:GOOG) has a long history of disruption and one that extends far beyond internet search and advertising. As such, it’s not surprising that the stock makes appearances in exchange traded funds such as the ARK Space Exploration and Innovation ETF (ARKX) and the ARK Autonomous Technology &…

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The History Of DNA Sequencing and Its Importance In Life Forms

DNA sequencing has helped develop various sectors of the economy and mainly in the health sector. DNA sequencing has helped scientists understand the causes of related genetic disorders and how to cure them. DNA sequencing has also helped scientists understand the evolution of different animal species. What about developing GMOs?…

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Pacific Biosciences hiring Bioinformatics Software Engineer in United States

PacBio’s Application Software Group focuses on building solid, strategic value around our core data type – highly accurate, long read sequencing – by producing innovative software that unlocks genomics in ways never seen before. We’re growing an interdisciplinary team of bioinformatic experts to tackle some of the most interesting problems…

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Assistant Research Professor – Genomics and Bioinformatics job with City of Hope

About City of Hope City 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 diseases and guided by a compassionate, patient-centered philosophy. Founded in 1913 and headquartered in Duarte, California, City of Hope…

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IPD values from ipdsummary, methylation analysis using PacBio

IPD values from ipdsummary, methylation analysis using PacBio 0 Is there anybody familiar with methylation analysis using PacBio data? I ran the ipdsummary tool from smrtlink package. The minimum coverage and p-value were set to 50X and 0.001, respectively. The methylation rate is about 2% of the total bases with…

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Startup BugSeq Bioinformatics Achieves High SARS-CoV-2 Detection Rate With Nanopore Sequencing

CHICAGO – Canadian startup BugSeq Bioinformatics has devised a method of detecting pathogens via metagenomic nanopore sequencing that the company says is more accurate and sensitive than PCR and microbial cultures. Notably, the technology does not need to target specific pathogens like PCR and microbial culture tests must. The firm…

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problems with snippy on galaxy

problems with snippy on galaxy 0 Hello I have a few questions regarding snippy. I need to analyze around 20 genomes and compare them to reference genome. I used unicycler to assemble my reference genome from illumina short reads and Pacbio long reads and then I used snippy to find…

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Introduction to DNA Sequencing Technology Part I

Location: 2240 CIEMAS During the past decade, a new generation of high-throughput DNA sequencers has transformed biomedical and biotechnology research. These new technologies have fostered the development of a wide range of applications to basic and clinical research, including SNP discovery, transcriptome profiling, genome sequencing, and epigenetics. The goal of…

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Advanced genomics research centre inaugurated

Next generation sequencing can bring about a revolution in biological sciences and unprecedented progress to society as genomics is the sunrise sector of the 21st century just like Information Technology in the 90s took the country to great heights, said Defence Minister Rajnath Singh on Thursday. Mr. Singh was speaking…

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How much would it cost to do a de novo assembly (plus annotation) of a jellifish genome?

How much would it cost to do a de novo assembly (plus annotation) of a jellifish genome? 0 I found this paper doi.org/10.1038/s41467-020-16801-9 and I was wondering how much their budget could have been per jellyfish. They’ve used PacBio and Hi-C data to generate a high-quality genome which is what…

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Interpretation of .gfa

Interpretation of .gfa 1 I love .gfa, but sometimes I have trouble to understand them. I have used Flye with pacBio reads with defaults options to make a first shot at assemble a linear bacterial genome. The genome probably contains some plasmids or some phages sequences. Flye gave me the…

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hisat2 compatibility for long read

hisat2 compatibility for long read 0 Hi, I am trying to align PacBio transcriptome reads against the genome to count the gene number. For pair end read i used the following workflow: # convert gff to gtf /home/software/cufflinks-2.2.1/gffread xxx.gff -T -o xxx.gtf # build index /home/software/hisat2-2.2.1/hisat2_extract_exons.py xxx.gtf > xxx.exon /home/software/hisat2-2.2.1/hisat2_extract_splice_sites.py…

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