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This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan Albert,
GitHub - quinlan-lab/STRling: Detect novel (and reference) STR expansions from short-read data (github.com)
STRling (pronounced like “sterling”) is a method to detect large STR expansions from short-read sequencing data.
submitted by: Istvan Albert
GitHub - j-andrews7/awesome-bioinformatics-benchmarks: A curated list of bioinformatics bench-marking papers and resources. (github.com)
A curated list of bioinformatics benchmarking papers and resources.
submitted by: Istvan Albert
recount3: summaries and queries for large-scale RNA-seq expression and splicing | Genome Biology | Full Text (genomebiology.biomedcentral.com)
We present recount3, a resource consisting of over 750,000 publicly available human and mouse RNA sequencing (RNA-seq) samples uniformly processed by our new Monorail analysis pipeline. To facilitate access to the data, we provide the recount3 and snapcount R/Bioconductor packages as well as complementary web resources. Using
aken together, our tools help biologists maximize the utility of publicly available RNA-seq data, especially to improve their understanding of newly collected data. recount3 is available from http://rna.recount.bio.
submitted by: Istvan Albert
Pangenome Graphs | Annual Review of Genomics and Human Genetics (www.annualreviews.org)
Pangenome graphs stand to become a ubiquitous tool in genomics. Although it is unclear whether they will replace linearreference genomes, their ability to harmoniously relate multiple sequence and coordinate systems will make them useful irrespective of which pangenomic models become most common in the future.
submitted by: Istvan Albert
Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs - PubMed (pubmed.ncbi.nlm.nih.gov)
Using a reference graph of 578 Escherichia coli genomes, we compare 20 diverse isolates. Pandora recovers more rare SNPs than single-reference-based tools, is significantly better than picking the closest RefSeq reference, and provides a stable framework for analyzing diverse samples without reference bias.
submitted by: Istvan Albert
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