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 Istvan Albert, and was edited by Istvan Albert,
https://academic.oup.com/bioinformatics/article/38/9/2617/6535233
BamToCov is a toolkit for rapid and flexible coverage computation that relies on the most memory efficient algorithm and is designed for integration in pipelines, given its ability to read alignment files from streams. The tools in the suite can process sorted BAM or CRAM files, allowing the user to extract coverage information via different filtering approaches and to save the output in different formats (BED, Wig or counts). The BamToCov algorithm can also handle strand-specific and/or physical coverage analyses.
submitted by: Istvan Albert
ScienceDirect (www.sciencedirect.com)
We propose a novel graph representation for highly accurate and long sequencing reads
It improves the efficiency of genome assembly and pangenome graph construction
We construct for the first time a pangenome of 661,405 bacterial genomes
See also:
https://www.sciencedirect.com/science/article/abs/pii/S2405471221003781
De novo assembled genomes serve as the backbone for modern genomics. In an article in this issue of Cell Systems, Ekim et al. present the mdBG assembler that can assemble genomes 100-fold faster than previous methods, including a human genome in under 10 min, which unlocks pan-genomics for many species.
submitted by: Istvan Albert
Benchmarking challenging small variants with linked and long reads: Cell Genomics
The Genome in a Bottle Consortium presents an expanded benchmark for 7 genomes
Long and linked reads expanded the benchmark to regions challenging for short reads
The expanded regions include challenging medically relevant genes like PMS2
This enables development of new technologies and bioinformatics methods
submitted by: Istvan Albert
With Quarto Coming, is R Markdown Going Away? No. - Yihui Xie | 谢益辉 (yihui.org)
So you have heard of Quarto, a new tool based on Pandoc for technical publishing. When you first see a .qmd document (Quarto), it looks quite similar to an .Rmd document (R Markdown), which can easily confuse R Markdown users. Questions can arise naturally: Why inventing a new system? Why cannot you just add the new features to the existing R Markdown ecosystem? Is R Markdown going to be retired? I will share some thoughts in this post.
submitted by: Istvan Albert
Quarto (quarto.org)
Quarto® is an open-source scientific and technical publishing system built on Pandoc
submitted by: Istvan Albert
What’s the BWA of CNV calling?
It still feels like a dark art where you need to roll your own.#Bioinformatics pic.twitter.com/SXFZGyyXYK
— Nils Homer (@nilshomer) April 13, 2022
What’s the BWA of CNV calling?
It still feels like a dark art where you need to roll your own.#Bioinformatics pic.twitter.com/SXFZGyyXYK
submitted by: Istvan Albert
GitHub - lskatz/Kalamari: A curated database of completed assemblies with taxonomy IDs (github.com)
Kalamari is a database of completed and public assemblies, backed by trusted institutions. These assemblies can be further used in formatted databases such as Kraken or Blast.
submitted by: Istvan Albert
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Thanks Istvan Albert ! Just a small correction on the link to Benchmarking challenging small variants with linked and long reads: Cell Genomics
ok, thanks for the note, corrected