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 GenoMax, Istvan Albert, and was edited by Istvan Albert,
GitHub - DecodeGenetics/Ratatosk: Hybrid error correction of long reads using colored de Bruijn graphs (github.com)
Ratatosk is a de novo error correction tool for erroneous long reads designed for accurate variant calling and assembly.
submitted by: Istvan Albert
GitHub - ivlachos/agamemnon: Accurate metagenomi/metatranscriptomic analysis pipeline (github.com)
AGAMEMNON is a comprehensive framework for the analysis of shotgun metagenomic/metatranscriptomic and host-specific RNA/DNA samples, enabling microbial quantification, differential abundance analyses and numerous exploratory visualizations.
submitted by: Istvan Albert
AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite | Genome Biology | Full Text (genomebiology.biomedcentral.com)
We introduce AGAMEMNON (https://github.com/ivlachos/agamemnon) for the acquisition of microbial abundances from shotgun metagenomics and metatranscriptomic samples, single-microbe sequencing experiments, or sequenced host samples. AGAMEMNON delivers accurate abundances at genus, species, and strain resolution.
submitted by: Istvan Albert
What is the cost of bioinformatics? A look at bioinformatics pricing and costs | by Karl Sebby | truwl | Feb, 2022 | Medium (medium.com)
A quite detailed rundown on the various costs associated with bioinformatics data analysis.
submitted by: Istvan Albert
https://academic.oup.com/genetics/advance-article-abstract/doi/10.1093/genetics/iyab227/6460343?redirectedFrom=fulltext
. In this study, we describe the assembly and annotation of a second individual genome, from a Puerto Rican individual whose DNA was collected as part of the Human Pangenome project. The new genome, called PR1, is the first true reference genome created from an individual of African descent. Due to recent improvements in both sequencing and assembly technology, and particularly to the use of the recently completed CHM13 human genome as a guide to assembly, PR1 is more complete and more contiguous than either GRCh38 or Ash1
submitted by: Istvan Albert
Competitive programming with AlphaCode | DeepMind (deepmind.com)
As part of DeepMind’s mission to solve intelligence, they have created a system called AlphaCode that writes computer programs at a competitive level.
submitted by: GenoMax
A Grammar of Graphics for Comparative Genomics • gggenomes (thackl.github.io)
gggenomes is a versatile graphics package for comparative genomics. It extends the popular R visualization packageggplot2 by adding dedicated plot functions for genes, syntenic regions, etc. and verbs to manipulate the plot to, for example, quickly zoom in into gene neighborhoods.
submitted by: Istvan Albert
GitHub - BrooksLabUCSC/flair: Full-Length Alternative Isoform analysis of RNA (github.com)
FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. FLAIR has primarily been used for nanopore cDNA, native RNA, and PacBio sequencing reads.
submitted by: Istvan Albert
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I'm surprised the
PR1genome paper isn't open access.