Bede Constantinides
@bede.im
Interested in infectious disease informatics. Research fellow at the University of Birmingham with @articnetwork.bsky.social. Also cycling, photography, active travel. https://bede.im
Pinned
Bede Constantinides
@bede.im
· Jun 13
Deacon: fast sequence filtering and contaminant depletion https://www.biorxiv.org/content/10.1101/2025.06.09.658732v1
New preprint! Deacon is a versatile tool for filtering FASTA/FASTQ files and streams at hundreds of megabases per second using minimizers, built with rapid metagenomic host depletion in mind, but equally useful for search.
github.com/bede/deacon
github.com/bede/deacon
Reposted by Bede Constantinides
Amazing novel mpox recombination between epidemic clade 1 and 2 in returning traveller detected in UK: virological.org/t/inter-clad...
Inter-Clade Recombinant Mpox Virus Detected in England in a Traveller Recently Returned from Asia
Inter-Clade Recombinant Mpox Virus Detected in England in a Traveller Recently Returned from Asia Authors: Steven T. Pullan1, Isobel Everall1, Rebecca Doherty1, Lucy Crossman1, Emma Wise1, Hassan Ha...
virological.org
December 8, 2025 at 6:17 PM
Amazing novel mpox recombination between epidemic clade 1 and 2 in returning traveller detected in UK: virological.org/t/inter-clad...
Reposted by Bede Constantinides
'Can you stop an outbreak becoming a pandemic?'
ARTIC Network recently delivered a workshop at the PHA4GE conference in Cape Town. Read more: www.linkedin.com/posts/artic-... @pha4ge.bsky.social
ARTIC Network recently delivered a workshop at the PHA4GE conference in Cape Town. Read more: www.linkedin.com/posts/artic-... @pha4ge.bsky.social
In October, as part of the Public Health Alliance for Genomic Epidemiology (PHA4GE) 2025 pre-conference schedule in Cape Town, the ARTIC team hosted a workshop titled “Can you stop an outbreak… | ARTI...
In October, as part of the Public Health Alliance for Genomic Epidemiology (PHA4GE) 2025 pre-conference schedule in Cape Town, the ARTIC team hosted a workshop titled “Can you stop an outbreak becomin...
www.linkedin.com
December 8, 2025 at 1:39 PM
'Can you stop an outbreak becoming a pandemic?'
ARTIC Network recently delivered a workshop at the PHA4GE conference in Cape Town. Read more: www.linkedin.com/posts/artic-... @pha4ge.bsky.social
ARTIC Network recently delivered a workshop at the PHA4GE conference in Cape Town. Read more: www.linkedin.com/posts/artic-... @pha4ge.bsky.social
"Prolonged exposure in shared, poorly ventilated spaces… drives respiratory virus transmission more than close contact."
www.nature.com/articles/s41...
www.nature.com/articles/s41...
The relative contribution of close-proximity contacts, shared classroom exposure and indoor air quality to respiratory virus transmission in schools - Nature Communications
The relative importance of close-proximity interactions, shared space and air quality to the transmission of respiratory viruses is not well understood. Here, the authors investigate this question by ...
www.nature.com
December 8, 2025 at 9:05 AM
"Prolonged exposure in shared, poorly ventilated spaces… drives respiratory virus transmission more than close contact."
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Bede Constantinides
We're half a decade into studies finding that improving airflow in classrooms will reduce disease transmission enormously, and that bleaching surfaces etc. does very little. And yet nothing changes. Waves of flu and colds wash over schools, and the schools pretend it's an act of God.
The relative contribution of close-proximity contacts, shared classroom exposure and indoor air quality to respiratory virus transmission in schools - Nature Communications
The relative importance of close-proximity interactions, shared space and air quality to the transmission of respiratory viruses is not well understood. Here, the authors investigate this question by ...
www.nature.com
December 8, 2025 at 4:23 AM
We're half a decade into studies finding that improving airflow in classrooms will reduce disease transmission enormously, and that bleaching surfaces etc. does very little. And yet nothing changes. Waves of flu and colds wash over schools, and the schools pretend it's an act of God.
Reposted by Bede Constantinides
And if you have a .fastq.gz.mim already present, you get another up to 2x speedup (or more with >6 cores).
December 7, 2025 at 11:54 PM
And if you have a .fastq.gz.mim already present, you get another up to 2x speedup (or more with >6 cores).
TIL Deacon decompresses fastq.gz 3x faster than GNU coreutils gzip/zcat.
You can decompress, dehost and recompress fastq.gz using Deacon in less time than only decompressing using coreutils gzip/zcat or pigz.
You can decompress, dehost and recompress fastq.gz using Deacon in less time than only decompressing using coreutils gzip/zcat or pigz.
December 7, 2025 at 10:58 PM
TIL Deacon decompresses fastq.gz 3x faster than GNU coreutils gzip/zcat.
You can decompress, dehost and recompress fastq.gz using Deacon in less time than only decompressing using coreutils gzip/zcat or pigz.
You can decompress, dehost and recompress fastq.gz using Deacon in less time than only decompressing using coreutils gzip/zcat or pigz.
Reposted by Bede Constantinides
github.com/bede/deacon
For anyone still using Bowtie2 for filtering or depletion of host sequences or specifics, I can recommend Deacon from @bedec.bsky.social . It is so much faster and easier than Bowtie2, and its performance is equal or better (tested with metagenomes and mitogenomes).🧬 & 🖥️
For anyone still using Bowtie2 for filtering or depletion of host sequences or specifics, I can recommend Deacon from @bedec.bsky.social . It is so much faster and easier than Bowtie2, and its performance is equal or better (tested with metagenomes and mitogenomes).🧬 & 🖥️
GitHub - bede/deacon: Fast DNA search and [host] depletion using minimizers
Fast DNA search and [host] depletion using minimizers - bede/deacon
github.com
December 3, 2025 at 7:40 PM
github.com/bede/deacon
For anyone still using Bowtie2 for filtering or depletion of host sequences or specifics, I can recommend Deacon from @bedec.bsky.social . It is so much faster and easier than Bowtie2, and its performance is equal or better (tested with metagenomes and mitogenomes).🧬 & 🖥️
For anyone still using Bowtie2 for filtering or depletion of host sequences or specifics, I can recommend Deacon from @bedec.bsky.social . It is so much faster and easier than Bowtie2, and its performance is equal or better (tested with metagenomes and mitogenomes).🧬 & 🖥️
Reposted by Bede Constantinides
Minimizer Density revisited: Models and Multiminimizers https://www.biorxiv.org/content/10.1101/2025.11.21.689688v1
November 22, 2025 at 2:47 AM
Minimizer Density revisited: Models and Multiminimizers https://www.biorxiv.org/content/10.1101/2025.11.21.689688v1
Reposted by Bede Constantinides
579 high-quality human genomes from @humanpangenome.bsky.social, Arab Pangenome and individual papers (CHM13, CN1, KSA001, I002C, YAO and KOREF1). Sequences available in the AGC format (3.7GB) and FM-index in the ropebwt3 format (20.3GB). For details, see github.com/lh3/human-asm
GitHub - lh3/human-asm: A collection of high-quality human genomes
A collection of high-quality human genomes. Contribute to lh3/human-asm development by creating an account on GitHub.
github.com
December 3, 2025 at 3:44 AM
579 high-quality human genomes from @humanpangenome.bsky.social, Arab Pangenome and individual papers (CHM13, CN1, KSA001, I002C, YAO and KOREF1). Sequences available in the AGC format (3.7GB) and FM-index in the ropebwt3 format (20.3GB). For details, see github.com/lh3/human-asm
Reposted by Bede Constantinides
Ok; mim (github.com/COMBINE-lab/...) preprint submitted! Excited for folks to see it and share thoughts. The key takeaway; mim allows the quick, one-time, building of a small auxiliary index that then allows scaling gzipped FASTQ parsing linearly in # of threads. 1/2
GitHub - COMBINE-lab/mim: A small, auxiliary index to massively improve parallel fastq parsing
A small, auxiliary index to massively improve parallel fastq parsing - COMBINE-lab/mim
github.com
November 25, 2025 at 2:13 PM
Ok; mim (github.com/COMBINE-lab/...) preprint submitted! Excited for folks to see it and share thoughts. The key takeaway; mim allows the quick, one-time, building of a small auxiliary index that then allows scaling gzipped FASTQ parsing linearly in # of threads. 1/2
Reposted by Bede Constantinides
@wytamma.bsky.social : so, it took a little bit of extra time (not the flight back from the CZI meeting), but I decided to just f#&$ing do it, and the basic code to build and parse with the auxiliary fastq index is working (github.com/COMBINE-lab/...). 1/2
GitHub - COMBINE-lab/mim: A small, auxiliary index to massively improve parallel fastq parsing
A small, auxiliary index to massively improve parallel fastq parsing - COMBINE-lab/mim
github.com
November 19, 2025 at 3:01 AM
@wytamma.bsky.social : so, it took a little bit of extra time (not the flight back from the CZI meeting), but I decided to just f#&$ing do it, and the basic code to build and parse with the auxiliary fastq index is working (github.com/COMBINE-lab/...). 1/2
Reposted by Bede Constantinides
New preprint: we looked into production of the bacterial toxin colibactin and found that MDR E. coli from the global north have co-evolved with endemic colibactin producers, acquiring colibactin resistance genes before undergoing clonal expansions.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Co-evolution between colibactin production and resistance is linked to clonal expansions in Escherichia coli
Specific strains of Escherichia coli employ the polyketide synthase island to produce a metabolite called colibactin that is implicated in colorectal tumorigenesis via its genotoxic effect on human DN...
www.biorxiv.org
November 18, 2025 at 6:41 AM
New preprint: we looked into production of the bacterial toxin colibactin and found that MDR E. coli from the global north have co-evolved with endemic colibactin producers, acquiring colibactin resistance genes before undergoing clonal expansions.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Bede Constantinides
I want to spell this out in case the implications aren't clear:
This means all public tools/webapps of GISAID data (all the ones you've been used to seeing thru the pandemic, as far as we can tell) are prohibited.
The file allowed this. Cut that - cut off all tools the public & others were using.
This means all public tools/webapps of GISAID data (all the ones you've been used to seeing thru the pandemic, as far as we can tell) are prohibited.
The file allowed this. Cut that - cut off all tools the public & others were using.
On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5
November 7, 2025 at 2:41 PM
I want to spell this out in case the implications aren't clear:
This means all public tools/webapps of GISAID data (all the ones you've been used to seeing thru the pandemic, as far as we can tell) are prohibited.
The file allowed this. Cut that - cut off all tools the public & others were using.
This means all public tools/webapps of GISAID data (all the ones you've been used to seeing thru the pandemic, as far as we can tell) are prohibited.
The file allowed this. Cut that - cut off all tools the public & others were using.
My account's upload and bulk download access were terminated permanently in 2021 without explanation after I published *checksums* of GISAID genomes. GISAID and its SAB have since ignored a dozen emails seeking explanation.
4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.
4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.
On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5
November 17, 2025 at 1:32 PM
My account's upload and bulk download access were terminated permanently in 2021 without explanation after I published *checksums* of GISAID genomes. GISAID and its SAB have since ignored a dozen emails seeking explanation.
4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.
4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.
Reposted by Bede Constantinides
I was on Last Word, the Radio 4 obituary programme, trying to sum up Jim Watson’s near-century long life.
Last Word - James Watson, Pauline Collins, Judith Vidal-Hall, Dugald Ross - BBC Sounds
Matthew Bannister on a scientist, an actor, a journalist and a fossil hunter.
www.bbc.co.uk
November 15, 2025 at 12:48 PM
I was on Last Word, the Radio 4 obituary programme, trying to sum up Jim Watson’s near-century long life.
Reposted by Bede Constantinides
Long term, good software requires lazy users: complain and file issues as soon as things don't work first try.
If nothing else, it means documentation should be improved.
If nothing else, it means documentation should be improved.
November 15, 2025 at 1:33 AM
Long term, good software requires lazy users: complain and file issues as soon as things don't work first try.
If nothing else, it means documentation should be improved.
If nothing else, it means documentation should be improved.
Reposted by Bede Constantinides
🔸️Early data suggests we could be in for a worse than normal flu season, brought on by a cluster of escape mutations in H3N2 this year that may lift the Re from 1.2 to 1.4. We are starting to see an uptick in the US. Data from BIOFIRE.
November 11, 2025 at 11:52 PM
🔸️Early data suggests we could be in for a worse than normal flu season, brought on by a cluster of escape mutations in H3N2 this year that may lift the Re from 1.2 to 1.4. We are starting to see an uptick in the US. Data from BIOFIRE.
Reposted by Bede Constantinides
New post from me, for UK folks only, on how you need to start preparing for Apple to switch off Advanced Data Protection and the end-to-end encryption of the data you store on it. Like I said, UK only. #SunlitUplands
heatherburns.tech/2025/11/10/t...
heatherburns.tech/2025/11/10/t...
Time to start de-Appling – Hi, I'm Heather Burns
heatherburns.tech
November 10, 2025 at 1:18 PM
New post from me, for UK folks only, on how you need to start preparing for Apple to switch off Advanced Data Protection and the end-to-end encryption of the data you store on it. Like I said, UK only. #SunlitUplands
heatherburns.tech/2025/11/10/t...
heatherburns.tech/2025/11/10/t...
Reposted by Bede Constantinides
As expected, unfortunately.
If ever you needed a reason for never using GISAID ever again (as a data producer or data user - we're both), look no further.
Time to move on to more trusted and transparent solutions.
If ever you needed a reason for never using GISAID ever again (as a data producer or data user - we're both), look no further.
Time to move on to more trusted and transparent solutions.
October 31, 2025 at 1:41 AM
As expected, unfortunately.
If ever you needed a reason for never using GISAID ever again (as a data producer or data user - we're both), look no further.
Time to move on to more trusted and transparent solutions.
If ever you needed a reason for never using GISAID ever again (as a data producer or data user - we're both), look no further.
Time to move on to more trusted and transparent solutions.
Reposted by Bede Constantinides
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 Bede Constantinides
“my brain is open” users.monash.edu/~normd/docum...
November 2, 2025 at 2:17 PM
“my brain is open” users.monash.edu/~normd/docum...
Reposted by Bede Constantinides
Really exciting that the preprint on Barbell, a new demultiplexer, is finally out!
It's the first tool that builds on Sassy, the approximate-DNA-searching tool that @rickbitloo.bsky.social and myself developed earlier this year, specifically with this application in mind.
It's the first tool that builds on Sassy, the approximate-DNA-searching tool that @rickbitloo.bsky.social and myself developed earlier this year, specifically with this application in mind.
Around 10% of your Nanopore reads (SQK-RBK114) are incorrectly trimmed. Here is why, and how our new tool Barbell solves it:
www.biorxiv.org/content/10.1...
Want to get started? github.com/rickbeeloo/b...
www.biorxiv.org/content/10.1...
Want to get started? github.com/rickbeeloo/b...
October 23, 2025 at 9:28 PM
Really exciting that the preprint on Barbell, a new demultiplexer, is finally out!
It's the first tool that builds on Sassy, the approximate-DNA-searching tool that @rickbitloo.bsky.social and myself developed earlier this year, specifically with this application in mind.
It's the first tool that builds on Sassy, the approximate-DNA-searching tool that @rickbitloo.bsky.social and myself developed earlier this year, specifically with this application in mind.
Reposted by Bede Constantinides
RIFs at CDC.
Destroying the Epidemic Intelligence Service, NCIRD, NCIPC & a dozen other areas/divisions/branches will cause enormous harm and suffering to America, and indeed to the whole world.
Call your Reps about it.
Then call them again.
Destroying the Epidemic Intelligence Service, NCIRD, NCIPC & a dozen other areas/divisions/branches will cause enormous harm and suffering to America, and indeed to the whole world.
Call your Reps about it.
Then call them again.
October 11, 2025 at 4:09 PM
RIFs at CDC.
Destroying the Epidemic Intelligence Service, NCIRD, NCIPC & a dozen other areas/divisions/branches will cause enormous harm and suffering to America, and indeed to the whole world.
Call your Reps about it.
Then call them again.
Destroying the Epidemic Intelligence Service, NCIRD, NCIPC & a dozen other areas/divisions/branches will cause enormous harm and suffering to America, and indeed to the whole world.
Call your Reps about it.
Then call them again.
Reposted by Bede Constantinides
Our recent paper on rifampicin resistant subpopulations in M. tuberculosis (M. tb) has been published at JAC-antimicrobial resistance.
I am really happy to see this work published just hours before submitting my DPhil thesis! 🔗👇
doi.org/10.1093/jaca...
I am really happy to see this work published just hours before submitting my DPhil thesis! 🔗👇
doi.org/10.1093/jaca...
Subpopulations in clinical samples of M. tuberculosis can give rise to rifampicin resistance and shed light on how resistance is acquired
AbstractObjectives. WGS has become a key tool for diagnosing Mycobacterium tuberculosis infections, but discrepancies between genotypic and phenotypic drug
doi.org
October 13, 2025 at 4:40 PM
Our recent paper on rifampicin resistant subpopulations in M. tuberculosis (M. tb) has been published at JAC-antimicrobial resistance.
I am really happy to see this work published just hours before submitting my DPhil thesis! 🔗👇
doi.org/10.1093/jaca...
I am really happy to see this work published just hours before submitting my DPhil thesis! 🔗👇
doi.org/10.1093/jaca...
Reposted by Bede Constantinides
For more information about the Friday night massacre at CDC, I wrote up an analysis of who got terminated and what that means for public health.
Grateful to @saveamericamvmt.bsky.social for supporting and amplifying. We are in really terrible trouble.
rasmussenretorts.substack.com/p/the-death-...
Grateful to @saveamericamvmt.bsky.social for supporting and amplifying. We are in really terrible trouble.
rasmussenretorts.substack.com/p/the-death-...
October 11, 2025 at 4:42 PM
For more information about the Friday night massacre at CDC, I wrote up an analysis of who got terminated and what that means for public health.
Grateful to @saveamericamvmt.bsky.social for supporting and amplifying. We are in really terrible trouble.
rasmussenretorts.substack.com/p/the-death-...
Grateful to @saveamericamvmt.bsky.social for supporting and amplifying. We are in really terrible trouble.
rasmussenretorts.substack.com/p/the-death-...