Microbial Assembly. This application generates de novo assemblies of small prokaryotic genomes between 1.9-10 Mb and companion plasmids between 2 – 220 kb. In addition it includes polishing and rotation of the origin of replication for each circular contig. Facilitates assembly of …
The SciLifeLab Bioinformatics platform offers a track where PhD students can get a senior bioinformatician as a personal advisor for up to two years of their PhD studies. We believe that the program will be an important part in building Swedish large-scale research competence in medicine and biology.
This goes through alignment, alignment quality control, data processing, variant calling, and variant filtration. Piper is pipeline project started at the SNP&SEQ Technology platform built on top of GATK Queue. Piper WholeGenome is for human whole genome sequencing data. Pipeline for quality control of Restriction-site Associated DNA sequencing (RAD-Seq). Genotyping-by-sequencing without prior genome information. Our in-house RAD-Seq pipeline for quality control of RAD-seq libraries. RAD-seq allows for deep yet sparsely sampled sequencing of many individuals in a highly multiplexed manner, where typical Introduction to Bioinformatics Using NGS Data.
21. CheckQC Quick quality control of Illumina runs. 90. Cluster Flow Simple pipelines for bioinformatics. We will build upon the infrastructures already existing within SciLifeLab for high-throughput sequencing (NGI/Clinical Genomics) and bioinformatics (NBIS). In the past 3 years, GAPS has brought together research groups from across Sweden who study the genetic basis of common diseases. SECAPR—a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments Andermann T, Cano Á, Zizka A, Bacon C, Antonelli A SRA: SRP131660 Zenodo: 10.5281/zenodo.1162653.
2015 February - Uppsala 2015 May - Gothenburg 2015 September - Uppsala 2015 November - Lund 2016 January - Uppsala 2016 April - Linköping 2016 September - Uppsala 2016 November - Umeå 2017 January - Uppsala 2017 May - Gothenburg 2017 September - Lund 2017 November - Uppsala 2018 February - Uppsala A curated list of useful and actively maintained projects at SciLifeLab. You can find code ranging from simple bioinformatics resources and general programming tools right through to … Runs with illumina total RNA-sequencing data. Aligns to the reference genome, gives QC metrics and finishes with gene count matrices.
Bioinformatics 34 (22) 3929-3930 [2018-11-15; online 2018-06-06] Fabien Burki. PubMed DOI Crossref. ST Spot Detector: a web-based application for automatic spot and tissue detection for spatial Transcriptomics image datasets. Wong K, Navarro JF, Bergenstråhle L, Ståhl PL, Lundeberg J.
This goes through alignment, alignment quality control, data processing, variant calling, and variant filtration. Piper is pipeline project started at the SNP&SEQ Technology platform built on top of GATK Queue. Piper WholeGenome is for human whole genome sequencing data. Pipeline for quality control of Restriction-site Associated DNA sequencing (RAD-Seq).
SciLifeLab Bioinformatics (NBIS) and Genomics (NGI) were both top-ranked in the recent VR evaluation (September 2017). “NBIS is probably the largest genuinely national and fully established bioinformatics infrastructure in Europe.” “[NBIS..] is crucial to the future competitiveness of Sweden in data-driven life
The support is fully subsidized and free of charge, but extensive hands-on involvement is required by the applying research groups. Note that a part of this call will focus on NBIS will enable world-class life science by providing expert knowledge, creative data integration, advanced training, efficient data publication and access to high-performance data and analysis methods.
Stockholm, Sweden. Bioinformatic researcher in Dr. Petter Brodin's Human Systems Immunology group
Title: SciLifeLab International Advisory Board – Report Appendices 2019 The SciLifeLab Data Center will try to integrate the bioinformatics
Links: SciLife Lab Stockholm · Tools of Science · Bioinformatics Infrastructure for Life Sciences(BILS).
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This is part of the Wallenberg foundation supported WABI program, an initiative that has been very helpful for us in previous projects.
Does SciLife lab provide Bioinformatic services? · 4. How do you apply
The Swedish Bioinformatics Advisory Program. Course date: 2017 - 2018.
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The Bioinformatics support at BEA includes assist with the design and analysis of next generation sequencing experiments. BEA provides consultation services for experimental design, analysis strategy, statistical considerations, price enquire and general help to select the appropriate analysis method. Many of BEA members have long experience in
Bioinformatics experts are then available to discuss your bioinformatics needs, free of charge. You can find the upcoming scheduled events on the NBIS events page.
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Science for Life Laboratory. We would like to invite you to a sneak peak of our new website before it goes live.
The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. Brief.
He has a PhD (2009) in Molecular Evolution focusing on gene and genome dynamics in host-adapted bacteria. After his PhD, Björn was hired to the SciLifeLab
Rediscovery rate estimation for assessing the validation of significant findings in high-throughput studies.
HiFi – 15-20X coverage for haploids or diploids.