Herald:The Biostar Herald for Monday, August 08, 2022
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8 weeks ago
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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, vdauwera, and was edited by Istvan Albert,

Tera Bio: Focus on your science (terra.bio)

The Terra blog covers a variety of topics in the life sciences, including useful bioinformatics resources, training opportunities, policy developments, new tools and capabilities, and behind the scenes stories from researchers and developers who are doing bioinformatics on the cloud.

submitted by: vdauwera

submitted by: Istvan Albert

Transcriptome variation in human tissues revealed by long-read sequencing | Nature (www.nature.com)

In this Article, we present a large human long-read RNA-seq dataset using the Oxford Nanopore Technologies platform from 88 samples from Genotype-Tissue Expression (GTEx) tissues and cell lines, complementing the GTEx resource. We identified just over 70,000 novel transcripts for annotated genes, and validated the protein expression of 10% of novel transcripts.

submitted by: Istvan Albert

submitted by: Istvan Albert

JBrowse 2: A modular genome browser with views of synteny and structural variation | bioRxiv (www.biorxiv.org)

We present JBrowse 2, a general-purpose genome annotation browser offering enhanced visualization of complex structural variation and evolutionary relationships. JBrowse 2 retains the core features of the open-source JavaScript genome browser JBrowse while adding new views for synteny, dotplots, breakpoints, gene fusions, and whole-genome overviews.

submitted by: Istvan Albert

Assembler artifacts include misassembly because of unsafe unitigs and under-assembly because of bidirected graphs (genome.cshlp.org)

We prove that, contrary to popular belief, even when there are no sequencing errors, unitigs are not always safe (i.e. they are not guaranteed to be substrings of the sequenced genome). We also prove that the unitigs of a bidirected de Bruijn graph are different from those of a doubled de Bruijn graph and, contrary to our expectations, result in under-assembly.

submitted by: Istvan Albert


Here we proposed Meta-Prism 2.0, a microbial community sample analysis method that has pushed the time and memory efficiency to a new limit without compromising accuracy. Based on sparse data structure, time-saving instruction pipeline, and SIMD optimization, Meta-Prism 2.0 has enabled ultra-fast, memory-efficient, flexible, and accurate search among millions of samples. Meta-Prism 2.0 was put to test on several data sets, with the largest containing 1 million samples.

submitted by: Istvan Albert

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