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,
AWS doesn't make sense for scientific computing (www.noahlebovic.com)
Scientific computing has a completely different usage profile than modern apps. Scientists need powerful computers and massive data transfer that runs on relatively simple infrastructure. Most cloud computing has infrastructural complexity that isn't necessary for scientific computing, and that complexity comes at a cost.
submitted by: Istvan Albert
Progress in quickly finding orthologs as reciprocal best hits: comparing blast, last, diamond and MMseqs2 | BMC Genomics | Full Text (bmcgenomics.biomedcentral.com)
Finding orthologs remains an important bottleneck in comparative genomics analyses. While the authors of software for the quick comparison of protein sequences evaluate the speed of their software and compare their results against the most usual software for the task, it is not common for them to evaluate their software for more particular uses, such as finding orthologs as reciprocal best hits (RBH). Here we compared RBH results obtained using software that runs faster than blastp. Namely, lastal, diamond, and MMseqs2.
submitted by: Istvan Albert
Illumina Dusts Off the Old Playbook | by Simon Barnett | Oct, 2022 | Medium (medium.com)
I believe the work Illumina team members have accomplished, especially during a pandemic, is nothing short of amazing. As the current unequivocal leader in sequencing, these technology improvements will be a tailwind for a life science industry in desperate need of a win. And for that, I’m very happy. Regardless of how market share shifts, competition is terrific for researchers, clinicians, and patients alike. We’ve not had competition in sequencing like this in over a decade.
submitted by: Istvan Albert
A survey of best practices for RNA-seq data analysis | Genome Biology | Full Text (genomebiology.biomedcentral.com)
We review all of the major steps in RNA-seq data analysis, including experimental design, quality control, read alignment, quantification of gene and transcript levels, visualization, differential gene expression, alternative splicing, functional analysis, gene fusion detection and eQTL mapping. We highlight the challenges associated with each step.
submitted by: Istvan Albert
Very excited to share our preprint presenting a NextFlow pipeline that call variants and calculate allele frequency from a pool of WGS to generate a background variant library.
A thread on why I think it matters! 🧵1/7https://t.co/nmtCyEmzUX pic.twitter.com/ImiLCduKgt
— Solenne Correard (@CorreardSolenne) October 6, 2022
Very excited to share our preprint presenting a NextFlow pipeline that call variants and calculate allele frequency from a pool of WGS to generate a background variant library.
A thread on why I think it matters! 🧵1/7https://t.co/nmtCyEmzUX pic.twitter.com/ImiLCduKgt
submitted by: Istvan Albert
GitHub - lskatz/fasten: Fasten toolkit, for streaming operations on fastq files (github.com)
Perform random operations on fastq files, using unix streaming. Secure your analysis with Fasten!
submitted by: Istvan Albert
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