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, and was edited by Istvan Albert,
Omics! Omics!: Element Unveils AVITI (omicsomics.blogspot.com)
Element Biosciences is launching their AVITI sequencing system today in a blitz of events.
AVITI is a desktop instrument priced at $289K, a bit below NextSeq 2000, which can run two flowcells entirely independently; two sequencers for the space and outlay of one. At a cost of $1680 of consumables a user can generate 800 million reads in 2x150 format in 48 hours – or about 5-7 dollars per gigabase if running around specifications.
submitted by: Istvan Albert
Software testing in microbial bioinformatics: a call to action | Microbiology Society (www.microbiologyresearch.org)
Despite these efforts, sustainability and reproducibility are major issues since continued validation through software testing is still not a widely adopted practice. Here, we report seven recommendations that help researchers implement software testing in microbial bioinformatics.
submitted by: Istvan Albert
Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data | Nature Methods (www.nature.com)
We introduce the alevin-fry framework for quantifying sc/snRNA-seq data. In addition to being faster and more memory frugal than other accurate quantification approaches, alevin-fry ameliorates the memory scalability and false-positive expression issues that are exhibited by other lightweight tools.
submitted by: Istvan Albert
Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses (genome.cshlp.org)
In order to find the best haploid genome representation, we constructed consensus genomes at the pan-human, super-population, and population levels, utilizing variant information from the 1000 Genomes Project. ... For reads overlapping homozygous variants, we found that the mapping error decreased by a factor of ~2-3 when the reference was replaced with the pan-human consensus genome.
submitted by: Istvan Albert
Explainable t-SNE for single-cell RNA-seq data analysis | bioRxiv (www.biorxiv.org)
submitted by: Mensur Dlakic
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