Herald:The Biostar Herald for Monday, May 02, 2022
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Biostar 860

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


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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