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,
What is KrakenUniq and why does it use HyperLogLog? A thread about bioinformatics software, the second in a series.
KrakenUniq (https://t.co/YRkxSgsnMT) is an improved version of Kraken, a widely used metagenomics program for classifying DNA sequences 1/14
— Steven Salzberg 💙💛 (@StevenSalzberg1) January 12, 2024
What is KrakenUniq and why does it use HyperLogLog? A thread about bioinformatics software, the second in a series.
KrakenUniq (https://t.co/YRkxSgsnMT) is an improved version of Kraken, a widely used metagenomics program for classifying DNA sequences 1/14
submitted by: Istvan Albert
Comparison of calling pipelines for whole genome sequencing: an empirical study demonstrating the importance of mapping and alignment | Scientific Reports (www.nature.com)
Rapid advances in high-throughput DNA sequencing technologies have enabled the conduct of whole genome sequencing (WGS) studies, and several bioinformatics pipelines have become available. The aim of this study was the comparison of 6 WGS data pre-processing pipelines, involving two mapping and alignment approaches (GATK utilizing BWA-MEM2 2.2.1, and DRAGEN 3.8.4) and three variant calling pipelines (GATK 4.2.4.1, DRAGEN 3.8.4 and DeepVariant 1.1.0). [..] Mapping and alignment played a key role in variant calling of WGS, with the DRAGEN outperforming GATK.
submitted by: Istvan Albert
https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btae014/7515251
In bioinformatics, multiple sequence alignment (MSA) is a crucial task. However, conventional methods often struggle with aligning ultralong sequences. To address this issue, researchers have designed MSA methods rooted in a vertical division strategy, which segments sequence data for parallel alignment. A prime example of this approach is FMAlign, which utilizes the FM-index to extract common seeds and segment the sequences accordingly.
submitted by: Istvan Albert
The impact of postdoctoral training on early careers in biomedicine | Nature Biotechnology (www.nature.com)
The biomedical research enterprise is in crisis. NIH funding rates are near historic lows, the age at which a scientist may attain an independent research career is high, and there are far fewer permanent academic positions than graduating PhDs. Exacerbating this crisis is the peculiar institution of postdoctoral training1,2,3,4,5,6,7,8. During the past two decades, official bodies have raised concerns about the working conditions, long hours, lack of benefits, and forced geographic mobility faced by postdocs, as well as the effects of postdoc jobs on families6,9,10,11,12,13,14,15. Here, we examine the incidence and duration of biomedical postdoc positions, and the associated benefits and costs to those taking such a position, in terms of early career outcomes of employment placement and earnings.
submitted by: Istvan Albert
What is PhyloCSF++? A short thread about bioinformatics software, perhaps the first in a series.
PhyloCSF++ is a recent C++ implementation, with new features, of a very useful tool called PhyloCSF 1/8
— Steven Salzberg 💙💛 (@StevenSalzberg1) January 9, 2024
What is PhyloCSF++? A short thread about bioinformatics software, perhaps the first in a series.
PhyloCSF++ is a recent C++ implementation, with new features, of a very useful tool called PhyloCSF 1/8
submitted by: Istvan Albert
https://academic.oup.com/bioinformatics/article/38/5/1440/6420698
PhyloCSF++ is an efficient and parallelized C++ implementation of the popular PhyloCSF method to distinguish protein-coding and non-coding regions in a genome based on multiple sequence alignments (MSAs). It can score alignments or produce browser tracks for entire genomes in the wig file format. Additionally, PhyloCSF++ annotates coding sequences in GFF/GTF files using precomputed tracks or computes and scores MSAs on the fly with MMseqs2.
submitted by: Istvan Albert
OmicVerse: A single pipeline for exploring the entire transcriptome universe | bioRxiv (www.biorxiv.org)
Single-cell sequencing is frequently marred by “interruptions” due to limitations in sequencing throughput, yet bulk RNA-seq may harbor these ostensibly “interrupted” cells. In response, we introduce the single cell trajectory blending from Bulk RNA-seq (BulkTrajBlend) algorithm, a component of the OmicVerse suite that leverages a Beta-Variational AutoEncoder for data deconvolution and graph neural networks for the discovery of overlapping community. This approach proficiently interpolates and restores the continuity of “interrupted” cells within single-cell RNA sequencing dataset. Furthermore, OmicVerse provides an extensive toolkit for bulk and single cell RNA-seq analysis, offering uniform access to diverse methodologies, streamlining computational processes, fostering exquisite data visualization, and facilitating the extraction of novel biological insights to advance scientific research.
submitted by: Istvan Albert
Just a moment... (www.nejm.org)
Placebo treatments have been reported to help patients with many diseases, but the quality of the evidence supporting this finding has not been rigorously evaluated.[...]We found little evidence in general that placebos had powerful clinical effects. Although placebos had no significant effects on objective or binary outcomes, they had possible small benefits in studies with continuous subjective outcomes and for the treatment of pain.
submitted by: Istvan Albert
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