Tag: aspera

Loeb, V. et al. Effects of sea-ice extent and krill or salp dominance on the Antarctic food web. Nature 387, 897–900 (1997). Article  ADS  CAS  Google Scholar  Atkinson, A., Siegel, V., Pakhomov, E. & Rothery, P. Long-term decline in krill stock and increase in salps within the Southern Ocean. Nature…

Abstract The European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI) is one of the world’s leading sources of public biomolecular data. Based at the Wellcome Genome Campus in Hinxton, UK, EMBL-EBI is one of six sites of the European Molecular Biology Laboratory (EMBL), Europe’s only intergovernmental life sciences organisation. This…

Image by Gerd Altmann from Pixabay For downloading data and standardized metadata from GEO (Gene Expression Omnibus) and SRA (Sequence Read Archive), several bioinformatics and command-line tools and scripts are available, primarily hosted on GitHub. ARA: An automated pipeline developed for better sampling of NCBI SRA database records, allowing full…

About the team/job The Cortes-Ciriano group co-leads the CRUK-funded Stratified Medicine Pediatrics Programme (SMPEDS). SMPEDS is the UK national molecular profiling platform for children with relapsed cancer and it successfully provides infrastructure to triage patients into clinical trials by identifying molecular abnormalities in rapid turnaround, with clinical reporting through a…

Enterprise Storage Forum content and product recommendations are editorially independent. We may make money when you click on links to our partners. Learn More. Object storage solutions are an effective solution to an increasingly common modern enterprise business need: how to capture and store the growing volumes of data they…

Primers, plasmids, bacterial strains, and growth conditions Primers, plasmids, and strains used in this study are listed in Tables S1–S3, respectively. Escherichia coli strains MG1655, DH10B, MDS42, and their derivates were cultured in LB medium at 37 °C, with shaking at 220 rpm. All the recombinants containing the temperature-sensitive pSC101-derived plasmid were cultured…

Tool:sra-explorer : find SRA and FastQ download URLs in a couple of clicks 0 Hi all, As a fun little side project I’ve made a web tool to find runs on the NCBI Sequence Read Archive (SRA) and fetch the download URLs for these. You can do all of this…

Editor’s Note: The following contains spoilers for Star Trek: Strange New Worlds Season 2. It didn’t take long in the second season of Star Trek: Strange New Worlds to return to a flashpoint surrounding the identity of one of its most prominent characters. Specifically, viewers were shown in the first…

PRESS RELEASE Published June 27, 2023 New Jersey, United States, Digital Journal/ Software asset management (SAM) tools automate many of the tasks required to maintain compliance with software licenses, thereby controlling software spending. They facilitate the in-depth analysis of software assets by decoding software license entitlements, automating the collection of…

Problem while downloading SRA using aspera links 1 while downloading fastq.gz files using aspera command in ubuntu, it’s showing an error message. Session Stop (Error: Server aborted session: No such file or directory) I checked using other aspera commands for fastq.gz files which i have dowloaded 2 weeks ago, same…

SRA download 0 I’m trying to download a lot of SRA files which are whole genome of animals. average sizes are tens of gigabytes so it takes almost a day to download one individual even if I use SRAtoolkit prefetch and than fasterq-dump. I know there are other ways like…

Unfortunately there is not enforced standard of what metadata must make into the SRA, it is very frustrating actually and makes reproducing any analysis needlessly complicated. You can look at what EBI fields are there, and sometimes they produce more fields than SRA: pip install bio then look at the…

1. Introduction Charophytes, extant and fossil members of the order Charales plus the members of the extinct orders Sycidiales and Moellerinales (Schneider et al., 2015) are algae with a complex morphology, which are closely related to modern land plants (Nishiyama et al., 2018). Taxa delineation of charophytes is commonly based on morphological…

Aspera: Command ‘ascp’ not found 1 I am trying to download files from the idr website using aspera. I am running the following command however I get the error Command ‘ascp’ not found. The ssh key exists and the file path is correct. ascp -TQ -l40m -P 33001 -i “path/to/key/asperaweb_id_dsa.openssh”…

This tiny tutorial cover setting up Aspera Connect (binary is called ascp) which might be used to download sequencing data, e.g. with download links provided by sra-explorer.info, see also sra-explorer : find SRA and FastQ download URLs in a couple of clicks Setting up Aspera Connect is simple and was…

Hi all, I’m trying to create a local nt blast database, my eventual goal is to create a subset based on a taxanomic group to be used on a cluster with limited storage space, its seems the only way to do this though is to start with the whole database…

Job Description Title: Bioinformatics NGS Data AnalystDuration: 12 monthsLocation: Remote Job Description:POSITION SUMMARY• Key member within the clinical imaging line within the Digital Medicine & Translational Imaging group, Early Clinical Development• Support the clinical image data management and analysis POSITION RESPONSIBILITIES• Work with Imaging Lead, Information Management – Clinical Trial…