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
At the beginning of 2018 at an @ENCODE_NIH meeting, the idea for the ENCODE Imputation Challenge was born: an open contest to predict genome-wide genomics experiments given fixed train/test sets and encourage development of large-scale imputation methods.
warning: drama 🧵
1/
— Jacob Schreiber (@jmschreiber91) August 3, 2022
At the beginning of 2018 at an @ENCODE_NIH meeting, the idea for the ENCODE Imputation Challenge was born: an open contest to predict genome-wide genomics experiments given fixed train/test sets and encourage development of large-scale imputation methods.
warning: drama 🧵
1/
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
Current #SingleCell pipelines overcluster, leading to over-reporting novel cell types. We present a statistical method to help determine which clusters are real. Can be applied to raw counts or existing clusters.
Code: https://t.co/BaSkBEz4s2
Preprint: https://t.co/IfBs3nHaBT
— Rafael Irizarry (@rafalab) August 3, 2022
Current #SingleCell pipelines overcluster, leading to over-reporting novel cell types. We present a statistical method to help determine which clusters are real. Can be applied to raw counts or existing clusters.
Code: https://t.co/BaSkBEz4s2
Preprint: https://t.co/IfBs3nHaBT
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
https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giac073/6651347
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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