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This edition of the Herald was brought to you by contribution from acvill, Istvan Albert, and was edited by Istvan Albert,
https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbac413/6702672?login=false
Here, we conducted a critical assessment of pan-genomics of MAGs, by comparing pan-genome analysis results of complete bacterial genomes and simulated MAGs. We found that incompleteness led to significant core gene (CG) loss. We conclude that lowering CG threshold and predicting genes in metagenome mode (as Anvi’o does with Prodigal) are necessary in pan-genome analysis of MAGs. Development of new pan-genome analysis tools specifically for MAGs are needed in future studies.
submitted by: Istvan Albert
The Era of Fast, Cheap Genome Sequencing Is Here | WIRED (www.wired.com)
Now, sequencing is about to get even cheaper. At an industry event in San Diego today, genomics behemoth Illumina unveiled what it calls its fastest, most cost-efficient sequencing machines yet, the NovaSeq X series. The company, which controls around 80 percent of the DNA sequencing market globally, believes its new technology will slash the cost to just $200 per human genome while providing a readout at twice the speed
submitted by: Istvan Albert
Metagenome analysis using the Kraken software suite | Nature Protocols (www.nature.com)
Our protocol describes the execution of the Kraken programs, via a sequence of easy-to-use scripts, in two scenarios: (1) quantification of the species in a given metagenomics sample; and (2) detection of a pathogenic agent from a clinical sample taken from a human patient. The protocol, which is executed within 1-2 h, is targeted to biologists and clinicians working in microbiome or metagenomics analysis who are familiar with the Unix command-line environment.
submitted by: Istvan Albert
On taming the effect of transcript level intra-condition count variation during differential expression analysis: A story of dogs, foxes and wolves | PLOS ONE (journals.plos.org)
We present TVscript, a tool that removes reference-based transcripts associated with intra-condition count variation above specified thresholds and we explore the effects of such variation on differential expression analysis.
submitted by: Istvan Albert
I made a tutorial on *GNU parallel* -- a new video on my OMGenomics channel covering everything you need to know to use GNU parallel painlessly, including an example of using parallel for launching bioinformatics jobs to a cloud or compute cluster.https://t.co/Fpnh6YOky7
— Maria Nattestad (@marianattestad) September 28, 2022
I made a tutorial on *GNU parallel* -- a new video on my OMGenomics channel covering everything you need to know to use GNU parallel painlessly, including an example of using parallel for launching bioinformatics jobs to a cloud or compute cluster.https://t.co/Fpnh6YOky7
— Maria Nattestad (@marianattestad) September 28, 2022submitted by: Istvan Albert
Benchmarking Oxford Nanopore Read Alignment-Based Structural Variant Detection Tools in Crop Plant Genomes | bioRxiv (www.biorxiv.org)
We used real and simulated Oxford Nanopore reads for two crops, allotetraploid Brassica napus (oilseed rape) and diploid Solanum lycopersicum (tomato), and evaluated several read aligners and SV callers across 5x, 10x, and 20x coverages typically used in re-sequencing studies. Our benchmarks provide a useful guide for designing Oxford Nanopore re-sequencing projects and SV discovery pipelines for crop plants.
submitted by: Istvan Albert
GitHub - kishwarshafin/pepper: PEPPER-Margin-DeepVariant (github.com)
PEPPER is a genome inference module based on recurrent neural networks that enables long-read variant calling and nanopore assembly polishing in the PEPPER-Margin-DeepVariant pipeline. This pipeline enables nanopore-based variant calling with DeepVariant.
submitted by: Istvan Albert
GitHub - acvill/CRISPRviewR: an R package for visualizing CRISPRs across environmental datasets (github.com)
CRISPRviewR is an R package that allows comparison and visualization of CRISPR arrays identified with minCED.
submitted by: acvill
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