Michael Hall
@mbhall88.bsky.social
Bioinformatics geek 🤓 crafting Rust-y tools 🦀 for microbial genomes 🦠 🧬.
Trying to master Dad mode 👨🍼
See what I'm up to here: https://github.com/mbhall88
Trying to master Dad mode 👨🍼
See what I'm up to here: https://github.com/mbhall88
Pinned
Genome size estimation from long read overlaps
AbstractMotivation. Accurate genome size estimation is an important component of genomic analyses such as assembly and coverage calculation, though existin
academic.oup.com
Our method for genome size estimation from long-read overlaps is now published 🥳
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
🚨 Update to nohuman 🚨
While testing against the standard Kraken DB, I noticed Kraken was detecting far more human reads than nohuman. I realised Kraken masks low-complexity regions by default during DB construction and that setting had been left on in nohuman, leading to missing human reads.
While testing against the standard Kraken DB, I noticed Kraken was detecting far more human reads than nohuman. I realised Kraken masks low-complexity regions by default during DB construction and that setting had been left on in nohuman, leading to missing human reads.
November 20, 2025 at 6:50 AM
🚨 Update to nohuman 🚨
While testing against the standard Kraken DB, I noticed Kraken was detecting far more human reads than nohuman. I realised Kraken masks low-complexity regions by default during DB construction and that setting had been left on in nohuman, leading to missing human reads.
While testing against the standard Kraken DB, I noticed Kraken was detecting far more human reads than nohuman. I realised Kraken masks low-complexity regions by default during DB construction and that setting had been left on in nohuman, leading to missing human reads.
Our method for genome size estimation from long-read overlaps is now published 🥳
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
Genome size estimation from long read overlaps
AbstractMotivation. Accurate genome size estimation is an important component of genomic analyses such as assembly and coverage calculation, though existin
academic.oup.com
November 7, 2025 at 3:19 AM
Our method for genome size estimation from long-read overlaps is now published 🥳
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
Reposted by Michael Hall
New from @dgpratas.bsky.social et al. for analyzing multiple sequences in multi-FASTA format using alignment-free methodologies. Scalable to millions of sequences for pandemic research and more
AltaiR: a C toolkit for alignment-free and temporal analysis of multi-FASTA data doi.org/10.1093/giga...
AltaiR: a C toolkit for alignment-free and temporal analysis of multi-FASTA data doi.org/10.1093/giga...
AltaiR: a C toolkit for alignment-free and temporal analysis of multi-FASTA data
AbstractBackground. Most viral genome sequences generated during the latest pandemic have presented new challenges for computational analysis. Analyzing mi
doi.org
December 12, 2024 at 10:29 AM
New from @dgpratas.bsky.social et al. for analyzing multiple sequences in multi-FASTA format using alignment-free methodologies. Scalable to millions of sequences for pandemic research and more
AltaiR: a C toolkit for alignment-free and temporal analysis of multi-FASTA data doi.org/10.1093/giga...
AltaiR: a C toolkit for alignment-free and temporal analysis of multi-FASTA data doi.org/10.1093/giga...
“Clarivate’s decision rewards journals for continuing the unhelpful practice of keeping peer review information hidden and unintentionally presenting incomplete and inadequate studies as sound science and punishes those journals that are more transparent.” 👏🙌
www.coalition-s.org/blog/how-the...
www.coalition-s.org/blog/how-the...
How the Web of Science takes a step back
<p>The Web of Science, a major commercial indexing service of scientific journals operated by Clarivate, recently decided to remove eLife from its Science Citation Index Expanded (SCIE). eLife will on...
www.coalition-s.org
December 3, 2024 at 9:49 AM
“Clarivate’s decision rewards journals for continuing the unhelpful practice of keeping peer review information hidden and unintentionally presenting incomplete and inadequate studies as sound science and punishes those journals that are more transparent.” 👏🙌
www.coalition-s.org/blog/how-the...
www.coalition-s.org/blog/how-the...
🌟 Excited to share my latest preprint with @lachlanjmc.bsky.social on @biorxivpreprint.bsky.social: "Genome size estimation from long read overlaps”! 🚀
Check it out here: doi.org/10.1101/2024...
And find the code here: github.com/mbhall88/lrge
🧵👇
Check it out here: doi.org/10.1101/2024...
And find the code here: github.com/mbhall88/lrge
🧵👇
doi.org
December 3, 2024 at 1:38 AM
🌟 Excited to share my latest preprint with @lachlanjmc.bsky.social on @biorxivpreprint.bsky.social: "Genome size estimation from long read overlaps”! 🚀
Check it out here: doi.org/10.1101/2024...
And find the code here: github.com/mbhall88/lrge
🧵👇
Check it out here: doi.org/10.1101/2024...
And find the code here: github.com/mbhall88/lrge
🧵👇
Props to eLife for sticking to their guns and essentially telling Clarivate "stuff your Journal Impact Factor, we don't want/need it and neither should anyone else".
Having recently published in eLife, I can attest to the fact that their review process is smooth and high quality.
Having recently published in eLife, I can attest to the fact that their review process is smooth and high quality.
As a long-term signatory of the Declaration on Research Assessment, we thank DORA for this supportive message. There has been an ongoing move away from journal-level metrics; we hope this will only accelerate now.
Publishing requires constant innovation and renewal to remain relevant. We are concerned by the action that Clarivate is taking in regard to @elife.bsky.social but not because eLife may not be eligible for an Impact Factor but because of the chilling effect on innovation. sfdora.org/2024/11/25/c...
December 2, 2024 at 12:37 AM
Props to eLife for sticking to their guns and essentially telling Clarivate "stuff your Journal Impact Factor, we don't want/need it and neither should anyone else".
Having recently published in eLife, I can attest to the fact that their review process is smooth and high quality.
Having recently published in eLife, I can attest to the fact that their review process is smooth and high quality.
Reposted by Michael Hall
Join the Interdisciplinary Postdoc Fellowship Program at the European Molecular Biology Laboratory (EMBL), one of the best places to do research in modern biology and develop your career.
Great opportunities for statisticians, comp. biologists, AI experts, mathem. modelers!
www.embl.org/eipod-linc
Great opportunities for statisticians, comp. biologists, AI experts, mathem. modelers!
www.embl.org/eipod-linc
November 22, 2024 at 9:02 AM
Join the Interdisciplinary Postdoc Fellowship Program at the European Molecular Biology Laboratory (EMBL), one of the best places to do research in modern biology and develop your career.
Great opportunities for statisticians, comp. biologists, AI experts, mathem. modelers!
www.embl.org/eipod-linc
Great opportunities for statisticians, comp. biologists, AI experts, mathem. modelers!
www.embl.org/eipod-linc
Handy tip of the day: Settings->Moderation->Muted words & tags->[enter last name of buffoon who is going to be president of USA]
🧘♂️
🧘♂️
November 21, 2024 at 11:18 PM
Handy tip of the day: Settings->Moderation->Muted words & tags->[enter last name of buffoon who is going to be president of USA]
🧘♂️
🧘♂️
For all you Pythonistas out there, if you haven't tried `uv` yet, give it a go. It will blow you mind 🤯 it is essentially `cargo` (from the Rust world) for Python! Amazing it took so long for the ecosystem to get here, but we did. Astral.sh are doing some incredible things, with incredible devs
November 20, 2024 at 10:31 PM
For all you Pythonistas out there, if you haven't tried `uv` yet, give it a go. It will blow you mind 🤯 it is essentially `cargo` (from the Rust world) for Python! Amazing it took so long for the ecosystem to get here, but we did. Astral.sh are doing some incredible things, with incredible devs
Reposted by Michael Hall
Microbial Genomics journal is looking for editors at senior level (functional genomics and microbe-host interactions) and handling editors (mainly eukaryotic microbial genomics but any within journal remit welcome). If you want to know more, let me know! microbiologysociety.org/who-we-are/j....
Jobs
View the current job vacancies at the Microbiology Society.
microbiologysociety.org
November 20, 2024 at 10:09 PM
Microbial Genomics journal is looking for editors at senior level (functional genomics and microbe-host interactions) and handling editors (mainly eukaryotic microbial genomics but any within journal remit welcome). If you want to know more, let me know! microbiologysociety.org/who-we-are/j....