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, natay,
In the poop of 11,810 people, scientists found 54,118 species of viruses, 92% of which were new to science. #planetofviruses https://t.co/LBFkwbyqRC
— Carl Zimmer (@carlzimmer) July 2, 2021
In the poop of 11,810 people, scientists found 54,118 species of viruses, 92% of which were new to science. #planetofviruses https://t.co/LBFkwbyqRC
— Carl Zimmer (@carlzimmer) July 2, 2021The gut microbiome is a complex microbial ecosystem with important roles in human health and development1. Although often overlooked, viruses are estimated to be abundant in the microbiome2,3 and have been associated with human disease4,5,6. In particular, bacteriophages (viruses that infect bacteria) constitute the majority of viral particles3,7,8 and can impact microbial ecosystem processes through phage predation9, lysogeny10 and horizontal gene transfer11.
submitted by: Istvan Albert
GitHub - COMBINE-lab/alevin-fry: 🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding. (github.com)
alevin-fry is a suite of tools for the rapid, accurate and memory-frugal processing single-cell and single-nucleus sequencing data. It consumes RAD files generated by salmon alevin, and performs common operations like generating permit lists, and estimating the number of distinct molecules from each gene within each cell. The focus in alevin-fry is on safety, accuracy and efficiency (in terms of both time and memory usage).
submitted by: Istvan Albert
It's mind-boggling to me how complex bioinformatics has gotten. I think modern software that abandoned the long-established tradition of Unix-centered CLI design was a giant mistake, and we're paying for it.
— Vince Buffalo (@vsbuffalo) July 4, 2021
It's mind-boggling to me how complex bioinformatics has gotten. I think modern software that abandoned the long-established tradition of Unix-centered CLI design was a giant mistake, and we're paying for it.
— Vince Buffalo (@vsbuffalo) July 4, 2021IMHO a natural consequence of journals accepting papers presenting yet another: "easy to use", "intuitive", "beginner-friendly", "foolproof", "convenient", bioinformatics pipeline.
submitted by: Istvan Albert
[2107.03611] Stool Studies Don't Pass the Sniff Test: A Systematic Review of Human Gut Microbiome Research Suggests Widespread Misuse of Machine Learning (arxiv.org)
While on this topic ... how many machine learning studies does it take to figure out that you need a proper validation for them as well:
Our findings cast serious doubt on the general validity of research claiming that the gut microbiome has high diagnostic or prognostic potential in human disease.
submitted by: Istvan Albert
Finally, the #flashbackFriday winner of the best proteomics tool name: the CRAPome, a repository of background contaminants for affinity purification-mass spectrometry. @gingraslab1 @nesvilab https://t.co/Ri26avCR3E
— Nature Methods (@naturemethods) May 28, 2021
Finally, the #flashbackFriday winner of the best proteomics tool name: the CRAPome, a repository of background contaminants for affinity purification-mass spectrometry. @gingraslab1 @nesvilab https://t.co/Ri26avCR3E
— Nature Methods (@naturemethods) May 28, 2021The "cringe-funny" flashback.
There was a time when Nature would publish a tool named like this ... think about that for a second.
submitted by: Istvan Albert
But that doesn’t help the sadness for the really useful tools in Picard that sometimes get overlooked for those in samtools and confused with those in GATK. And to all my tools now in the graveyard, I really tried. Hopefully the field is better for them… pic.twitter.com/e4LnZsezjt
— Nils Homer (@nilshomer) July 11, 2021
But that doesn’t help the sadness for the really useful tools in Picard that sometimes get overlooked for those in samtools and confused with those in GATK. And to all my tools now in the graveyard, I really tried. Hopefully the field is better for them… pic.twitter.com/e4LnZsezjt
— Nils Homer (@nilshomer) July 11, 2021The world of bioinformatics can be unfair - yet the comments have several notable reactions that may explain the reasons:
"GATK and Picard are so intertwined, with so many functions now, that unless you are a Broad scientist with a staff of dozens to help you navigate it, its just "scary". "
or
" I know very few people outside of human genomics that use Picard (heaven forbid GATK) and samtools is just the go-to option"
submitted by: Istvan Albert
Release 1.13 · samtools/samtools · GitHub (github.com)
Notable changes:
- A new tool, samtools import, has been added. It reads one or more FASTQ files and converts them into unmapped SAM, BAM or CRAM.
- Three new counts have been added to samtools flagstat: primary, mapped primary and duplicate primary.
- Complete rewrite of samtools depth. This means it is now considerably faster and does not need a depth limit to avoid high memory usage.
submitted by: Istvan Albert
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