Herald:The Biostar Herald for Monday, October 31, 2022

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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,

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Ultrafast functional profiling of RNA-seq data for nonmodel organisms (genome.cshlp.org)

We have developed Seq2Fun, a novel, all-in-one, ultrafast tool to directly perform functional quantification of RNA-seq reads without transcriptome de novo assembly. The pipeline starts with raw read quality control: sequencing error correction, removing poly(A) tails, and joining overlapped paired-end reads. It then conducts a DNA-to-protein search by translating each read into all possible amino acid fragments and subsequently identifies possible homologous sequences in a well-curated protein database.

submitted by: Istvan Albert

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Scientific Publishing: Peer review without gatekeeping | eLife (elifesciences.org)

eLife is changing its editorial process to emphasize public reviews and assessments of preprints by eliminating accept/reject decisions after peer review.

submitted by: Istvan Albert

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(1) The cloud is really designed to suck finances from customers. Very poor cost management tooling especially for academic labs who live on tight budgets. I used to be quite bullish about cloud. Learned my lesson the hard way. 9/

— Anshul Kundaje (Glory to 🇺🇦) (@anshulkundaje) July 25, 2022

submitted by: Istvan Albert

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If you’d like to checkout human data for the brand new @PacBio Revio platform here it is: https://t.co/zxEVrRzH5C

— Zev Kronenberg (@zevkronenberg) October 26, 2022

submitted by: Istvan Albert

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HiFi metagenomic sequencing enables assembly of accurate and complete genomes from human gut microbiota | Nature Communications (www.nature.com)

Metagenome-assembled genomes (MAGs) often suffer from fragmentation and chimerism. Recently, 20 complete MAGs (cMAGs) have been assembled from Oxford Nanopore long-read sequencing of 13 human fecal samples, but with low nucleotide accuracy. Here, we report 102 cMAGs obtained by Pacific Biosciences (PacBio) high-accuracy long-read (HiFi) metagenomic sequencing of five human fecal samples, whose initial circular contigs were selected for complete prokaryotic genomes using our bioinformatics workflow.

submitted by: Istvan Albert

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PacBio Revio: Long-read sequencing at scale (www.pacb.com)

PacBio announces Revio:

Revio system delivers 360 Gb of HiFi reads per day, equivalent to 1,300 human whole genomes per year. ​

submitted by: Istvan Albert

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https://osf.io/preprints/metaarxiv/cd5j9/

While not specifically bioinformatics in its topic many of the findings ring true:

This study explores how researchers’ analytical choices affect the reliability of scientific findings.

Most discussions of reliability problems in science focus on systematic biases. We broaden the lens to include conscious and unconscious decisions that researchers make during data analysis and that may lead to diverging results.

Researchers’ expertise, prior beliefs, and expectations barely predicted the wide variation in research outcomes. More than 90% of the total variance in numerical results remained unexplained even after accounting for research decisions identified via qualitative coding of each team’s workflow. This reveals a universe of uncertainty that is hidden when considering a single study in isolation. The idiosyncratic nature of how researchers’ results and conclusions varied is a new explanation for why many scientific hypotheses remain contested. It calls for greater humility and clarity in reporting scientific findings

submitted by: Istvan Albert

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