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,
https://academic.oup.com/bioinformatics/article/38/21/4994/6694040
Here, we argue that in the majority of bioinformatics settings, available experimental data do not have the size, resolution and sufficient set of controls (hereafter referred to as ‘limited data’) that would allow for rigorous method assessment.
Method developers should be encouraged to make use of both simulated and experimental data, in complementary ways, to cover the multiple purposes of method assessment.
submitted by: Istvan Albert
42basepairs (42basepairs.com)
A better way to explore genomics data in the cloud.
submitted by: Istvan Albert
Excited to launch https://t.co/rjElBOglZk, a free platform for exploring genomics data (anything public on AWS, GCP)
Featuring:
- Interactive previews
- Sub-sampling
- Grouped indexes for .bam/.bai, etc
- IGV integration
- Interpreted CIGAR strings, SAM flags, quality scores pic.twitter.com/AR7pp0hG9c
— Robert Aboukhalil (@RobAboukhalil) November 2, 2022
Excited to launch https://t.co/rjElBOglZk, a free platform for exploring genomics data (anything public on AWS, GCP)
Featuring:
- Interactive previews
- Sub-sampling
- Grouped indexes for .bam/.bai, etc
- IGV integration
- Interpreted CIGAR strings, SAM flags, quality scores pic.twitter.com/AR7pp0hG9c
submitted by: Istvan Albert
GitHub - dutilh/CAT: CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) (github.com)
Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against a protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. CAT and BAT can be run from intermediate steps if files are formated appropriately
submitted by: Istvan Albert
Peer Review: First results from a trial at eLife | Inside eLife | eLife (elifesciences.org)
New approach to peer review proves popular with authors, with very similar acceptance rates for male and female last authors, but with higher acceptance rates for late-career researchers compared to their early- and mid-career colleagues.
submitted by: Istvan Albert
Significant variation in the performance of DNA methylation predictors across data preprocessing and normalization strategies | Genome Biology | Full Text (genomebiology.biomedcentral.com)
DNA methylation (DNAm)-based predictors hold great promise to serve as clinical tools for health interventions and disease management. While these algorithms often have high prediction accuracy, the consistency of their performance remains to be determined. We therefore conduct a systematic evaluation across 101 different DNAm data preprocessing and normalization strategies and assess how each analytical strategy affects the consistency of 41 DNAm-based predictors.
submitted by: Istvan Albert
Want to get the Biostar Herald in your email? Who wouldn't? Sign up righ'ere: toggle subscription
