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,
Genomic variant benchmark: if you cannot measure it, you cannot improve it | Genome Biology | Full Text (genomebiology.biomedcentral.com)
Genomic benchmark datasets are essential to driving the field of genomics and bioinformatics. [..] In this review, we discuss the available benchmark datasets and their utility. Additionally, we focus on the most recent benchmark of genes with medical relevance and challenging genomic complexity.
submitted by: Istvan Albert
piscem-infer 0.3 documentation (piscem-infer.readthedocs.io)
piscem-infer is a tool to perform quantification of some target (e.g. transcripts in RNA-seq, strains or species in metagenomic sequencing) using statistical inference to arrive at an abundance estimate for each target and, optionally, an associated uncertainty for each estimate.
submitted by: Istvan Albert
Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures | Nature Methods (www.nature.com)
Samples were deeply sequenced on both Illumina short-read and Oxford Nanopore Technologies long-read platforms. Alongside the ground-truth available via the sequins, we created in silico mixture samples to allow performance assessment in the absence of true positives or true negatives. Our results show that StringTie2 and bambu outperformed other tools from the six isoform detection tools tested, DESeq2, edgeR and limma-voom were best among the five differential transcript expression tools tested and there was no clear front-runner for performing differential transcript usage analysis between the five tools compared, which suggests further methods development is needed for this application.
submitted by: Istvan Albert
The status of the human gene catalogue | Nature (www.nature.com)
Here we review the status of the human gene catalogue and the efforts to complete it in recent years.
submitted by: Istvan Albert
We have a cool new tool (in @rustlang) for bulk seq-based quantification brewing https://t.co/msVFZl2UgR. It should work well for #RNAseq quant, metagenomic abundance est. & related problems. Will put up quickstart guide soon for those interested in testing. Feedback welcome!
— 𝕐 (@rob@genomic.social) (@nomad421) September 30, 2023
We have a cool new tool (in @rustlang) for bulk seq-based quantification brewing https://t.co/msVFZl2UgR. It should work well for #RNAseq quant, metagenomic abundance est. & related problems. Will put up quickstart guide soon for those interested in testing. Feedback welcome!
— 𝕐 (@rob@genomic.social) (@nomad421) September 30, 2023submitted by: Istvan Albert
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