Pierre Lindenbaum#alphagenome: what is the 'best' variant of interest ? I asked #biostars : https://www.biostars.org/p/9618109/
"Q: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 2025 ?" https://www.biostars.org/p/9616981/
I asked #biostars : "Parabricks : Number of GPUs requested (2) is more than number of GPUs (0) in the system., exiting."
https://www.biostars.org/p/9614740/
#bioinformatics #parabricks #NVIDIA #haplotypecaller #gatk #gpus
"AliNe is a pipeline written in Nextflow that aims to efficiently align reads against a reference genome using the tools of your choice." (via #biostars ) https://github.com/Juke34/AliNe
The GIAB genomic stratifications resource for human reference genomes(via #biostars) https://www.nature.com/articles/s41467-024-53260-y "Here we describe a set of “stratifications,” which are BED files that define distinct contexts throughout the genome. We define these for GRCh37/38 as well as the new T2T-CHM13 reference, adding many new hard-to-sequence regions which are critical for understanding performance as the field progresses"
The GIAB genomic stratifications resource for human reference genomes - Nature Communications
The GIAB genomic stratification resource defines challenging regions in three commonly used human genome references, including the first complete human genome (CHM13). These help understand strengths and weaknesses of sequencing and analysis methods.
asked #biostars : "finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"" https://www.biostars.org/p/9595035/ #uORF #mass #masspec #spectrometry #translation #UTR #ORF
VCF2PCACluster: a simple, fast and memory-efficient tool for principal component analysis of tens of millions of SNPs https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-024-05770-1 (via #biostars)
VCF2PCACluster: a simple, fast and memory-efficient tool for principal component analysis of tens of millions of SNPs - BMC Bioinformatics
Principal component analysis (PCA) is an important and widely used unsupervised learning method that determines population structure based on genetic variation. Genome sequencing of thousands of individuals usually generate tens of millions of SNPs, making it challenging for PCA analysis and interpretation. Here we present VCF2PCACluster, a simple, fast and memory-efficient tool for Kinship estimation, PCA and clustering analysis, and visualization based on VCF formatted SNPs. We implemented five Kinship estimation methods and three clustering methods for its users to choose from. Moreover, unlike other PCA tools, VCF2PCACluster possesses a clustering function based on PCA result, which enabling users to automatically and clearly know about population structure. We demonstrated the same accuracy but a higher performance of this tool in performing PCA analysis on tens of millions of SNPs compared to another popular PLINK2 software, especially in peak memory usage that is independent of the number of SNPs in VCF2PCACluster.
":F*up Night style events for #Bioinformatics ? " https://www.biostars.org/p/9591237/#9591239 #biostars "Have you ever made such an embarrassing bioinformatics mistake that you never dared to tell a soul about -- except maybe over drinks or other intoxicating substance?"
> Clinical bioinformatics nowadays have a lot of plenty tools like xxxx so I do not plan to waste time of my students with archaic command line pipelines.
😵 😂 😱