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This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan Albert,
The complete sequence of a human Y chromosome | Nature (www.nature.com)
Here, the Telomere-to-Telomere (T2T) consortium presents the complete 62,460,029-base-pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference, showing the complete ampliconic structures of gene families TSPY, DAZ and RBMY; 41 additional protein-coding genes, mostly from the TSPY family; and an alternating pattern of human satellite 1 and 3 blocks in the heterochromatic Yq12 region.
submitted by: Istvan Albert
Why so many names for the same contig? Isn't CM000664.2 just chr2?
Don't panic, we've got a tool for this.
fgbio CollectAlternateContigNames#Bioinformatics https://t.co/rfjqRf7Sna
— Nils Homer (@nilshomer) August 24, 2023
Why so many names for the same contig? Isn't CM000664.2 just chr2?
Don't panic, we've got a tool for this.
fgbio CollectAlternateContigNames#Bioinformatics https://t.co/rfjqRf7Sna
submitted by: Istvan Albert
The CUT&RUN suspect list of problematic regions of the genome | Genome Biology | Full Text (genomebiology.biomedcentral.com)
While CUT&RUN obtains similar results to ChIP-seq, its biochemistry and subsequent data analyses are different. We found that this results in a CUT&RUN-specific set of undesired high-signal regions.
submitted by: Istvan Albert
https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btad480/7234613
In this review, we evaluate short-read aligner performance with the goal of optimizing germline variant calling accuracy. We examine the performance of three general-purpose short-read aligners – BWA-MEM, Bowtie 2, and Arioc – in conjunction with three germline variant callers: DeepVariant, FreeBayes, and GATK HaplotypeCaller. We discuss the behavior of the read aligners with regard to the data elements on which the variant callers rely, and illustrate how the runtime configurations of these software tools combine to affect variant calling performance.
submitted by: Istvan Albert
"Data visualization is where you start and end a data analysis." -- @rafalab #JSM2023
— Stephanie Hicks (@stephaniehicks) August 8, 2023
"Data visualization is where you start and end a data analysis." -- @rafalab #JSM2023
— Stephanie Hicks (@stephaniehicks) August 8, 2023submitted by: Istvan Albert
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