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 Albert,
GitHub - Nextomics/NextDenovo: Fast and accurate de novo assembler for long reads (github.com)
NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a "correct-then-assemble" strategy similar to canu (no correction step for PacBio HiFi reads), but requires significantly less computing resources and storages. After assembly, the per-base accuracy is about 98-99.8%
submitted by: Istvan Albert
Release of DeepVariant v1.5
Added a model to call variants with ONT R10 simplex and duplex data
Added support for Element Biosciences data with WGS model
Added Revio data for training of PacBio model. Improved accuracy for PacBio (~4% error reduction)https://t.co/46U7hwXpdt
— Andrew Carroll (@acarroll_ATG) February 28, 2023
Release of DeepVariant v1.5
Added a model to call variants with ONT R10 simplex and duplex data
Added support for Element Biosciences data with WGS model
Added Revio data for training of PacBio model. Improved accuracy for PacBio (~4% error reduction)https://t.co/46U7hwXpdt
submitted by: Istvan Albert
Release DeepVariant 1.5.0 · google/deepvariant · GitHub (github.com)
DeepVariant 1.5.0 released
submitted by: Istvan Albert
Running accurate, comprehensive, and efficient genomics workflows on AWS using Illumina DRAGEN v4.0 | AWS HPC Blog (aws.amazon.com)
In this blog, we provide a walkthrough of running DRAGEN on AWS and highlight our results from the DRAGEN v4.0 DNA sequencing pipeline showing that, in addition to accuracy and efficiency, it supports the most comprehensive suite of tools for DNA sequencing, including copy number analysis, structural variants, SMN callers, repeat expansion detection, and pharmacogenomics insights for complex genes.
submitted by: Istvan Albert
Centrifuge+: improving metagenomic analysis upon Centrifuge | bioRxiv (www.biorxiv.org)
Here, we present Centrifuge+, which introduces unique mapping rate to describe the influence of similarities among species in the reference database when analyzing ambiguous reads. In contrast to the popular Centrifuge, Centrifuge+ improved the accuracy of abundance estimation on simulated reads from 4278 complete prokaryotic genomes.
submitted by: Istvan Albert
It's been a busy month at ATCC - we released over 200 new genomes to the ATCC Genome Portal!
Wohoo! Please RT!
💪🚀🦠🧬https://t.co/WRnrXZc8lM CC: @officialATCC @ATCCGenomics #genomics #bioinformatics
— Jonathan Jacobs (@bioinformer) February 28, 2023
It's been a busy month at ATCC - we released over 200 new genomes to the ATCC Genome Portal!
Wohoo! Please RT!
💪🚀🦠🧬https://t.co/WRnrXZc8lM CC: @officialATCC @ATCCGenomics #genomics #bioinformatics
submitted by: Istvan Albert
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