Florian Trigodet
@floriantrigodet.bsky.social
Computational microbiologist. Senior scientist at the Helmholtz Institute for Functional Marine Biodiversity, Oldenburg.
Working in Meren lab.
Working in Meren lab.
See this tutorial by Iva Veseli: anvio.org/tutorials/fm...
It contains everything you described above
It contains everything you described above
An exercise on metabolic reconstruction in anvi'o
A tutorial on how to run metabolism estimation and enrichment in anvi'o
anvio.org
October 8, 2025 at 7:50 AM
See this tutorial by Iva Veseli: anvio.org/tutorials/fm...
It contains everything you described above
It contains everything you described above
With anvi'o you can annotate genomes with multiple annotation sources, including KEGG KOfams.
Anvi'o also include a set of tool to compute metabolic module completeness and copy/numbers (useful for metagenomics).
Better: there is a program to compare func and metabolic enrichment
Anvi'o also include a set of tool to compute metabolic module completeness and copy/numbers (useful for metagenomics).
Better: there is a program to compare func and metabolic enrichment
October 8, 2025 at 7:49 AM
With anvi'o you can annotate genomes with multiple annotation sources, including KEGG KOfams.
Anvi'o also include a set of tool to compute metabolic module completeness and copy/numbers (useful for metagenomics).
Better: there is a program to compare func and metabolic enrichment
Anvi'o also include a set of tool to compute metabolic module completeness and copy/numbers (useful for metagenomics).
Better: there is a program to compare func and metabolic enrichment
I briefly used myloasm on a small project and I found the same read clipping issues as we reported for other assemblers like metaMDBG. Haven't had the time to run a full scale analysis like we did in our preprint.
September 24, 2025 at 12:05 PM
I briefly used myloasm on a small project and I found the same read clipping issues as we reported for other assemblers like metaMDBG. Haven't had the time to run a full scale analysis like we did in our preprint.
In the end, the truth should be in the reads and if multiple long (or short) reads support the joining of two genomic sequence with different GC content, skew, etc; then I would be inclined to trust its reality
April 29, 2025 at 3:51 PM
In the end, the truth should be in the reads and if multiple long (or short) reads support the joining of two genomic sequence with different GC content, skew, etc; then I would be inclined to trust its reality
(if all of them happens at the same genomic loci, I would have no doubt that it a case of a chimeric contig)
April 29, 2025 at 3:49 PM
(if all of them happens at the same genomic loci, I would have no doubt that it a case of a chimeric contig)
But all of them can occur naturally: recent genomic rearrangement creates shifts in GC skew; GC content can change with HGT or non-coding genes like rRNA; non-specific read recruitment and hypervariable region (insertion/deletion of genes) creates drops in coverage
April 29, 2025 at 3:47 PM
But all of them can occur naturally: recent genomic rearrangement creates shifts in GC skew; GC content can change with HGT or non-coding genes like rRNA; non-specific read recruitment and hypervariable region (insertion/deletion of genes) creates drops in coverage
GC skew is a great idea and I think a combination of GC skew, sharp change in GC content and drop of coverage would be great indicators to find chimeric sequences. Especially if they all occurs at the same genomic location
April 29, 2025 at 3:45 PM
GC skew is a great idea and I think a combination of GC skew, sharp change in GC content and drop of coverage would be great indicators to find chimeric sequences. Especially if they all occurs at the same genomic location
Thanks a lot for going through it in your journal club! The details of my blast search can be found here: tinyurl.com/ynxwsvwc
In short, I remove the DUST filter and I ask BLAST to only report the first hit. I don't know how it would report no hits if too many hits?
In short, I remove the DUST filter and I ask BLAST to only report the first hit. I don't know how it would report no hits if too many hits?
A reproducible workflow for Trigodet et al., 2025
A bioinformatics workflow for our study long-read assemblers
tinyurl.com
April 29, 2025 at 3:37 PM
Thanks a lot for going through it in your journal club! The details of my blast search can be found here: tinyurl.com/ynxwsvwc
In short, I remove the DUST filter and I ask BLAST to only report the first hit. I don't know how it would report no hits if too many hits?
In short, I remove the DUST filter and I ask BLAST to only report the first hit. I don't know how it would report no hits if too many hits?
Misreporting non-circular elements as circular can quickly deteriorate public genome databases. We hope we can work together to ensure assemblers include stricter checks, or offer modes that prioritize caution. We would love to hear your experiences or thoughts!
April 28, 2025 at 8:08 AM
Misreporting non-circular elements as circular can quickly deteriorate public genome databases. We hope we can work together to ensure assemblers include stricter checks, or offer modes that prioritize caution. We would love to hear your experiences or thoughts!
We hope to help the community to understand potential issues they may run into, and help the developers to see different perspectives. We have a fully reproducible bioinformatics workflow, and it is easy to add one more assembler to it, or new datasets:
merenlab.org/data/benchma...
merenlab.org/data/benchma...
A reproducible workflow for Trigodet et al., 2025
A bioinformatics workflow for our study long-read assemblers
merenlab.org
April 28, 2025 at 8:08 AM
We hope to help the community to understand potential issues they may run into, and help the developers to see different perspectives. We have a fully reproducible bioinformatics workflow, and it is easy to add one more assembler to it, or new datasets:
merenlab.org/data/benchma...
merenlab.org/data/benchma...
We are aware that developing assembly algorithms, especially for metagenomes, is a notoriously complex and difficult task, and we have a deep appreciation of those who invest their time and skills in creating and maintaining them. A heartfelt THANK YOU. We're here to help, nothing more.
April 28, 2025 at 8:08 AM
We are aware that developing assembly algorithms, especially for metagenomes, is a notoriously complex and difficult task, and we have a deep appreciation of those who invest their time and skills in creating and maintaining them. A heartfelt THANK YOU. We're here to help, nothing more.
And we observed astonishing number of repeats in results. Repeats are common in nature and the improved ability to resolve repeats is one of the strengths of long-read sequencing. But the repeats we found didn't look convincing and likely underlined other issues.
April 28, 2025 at 8:08 AM
And we observed astonishing number of repeats in results. Repeats are common in nature and the improved ability to resolve repeats is one of the strengths of long-read sequencing. But the repeats we found didn't look convincing and likely underlined other issues.
Accurate reconstruction of genomic variation is essential to associate within-population structural differences to ecological or evolutionary phenotypes. But we observed serious haplotyping errors, where assemblers created chimeric constructs or did things biologists wouldn't expect.
April 28, 2025 at 8:08 AM
Accurate reconstruction of genomic variation is essential to associate within-population structural differences to ecological or evolutionary phenotypes. But we observed serious haplotyping errors, where assemblers created chimeric constructs or did things biologists wouldn't expect.
We observed cases of premature circularization. VERY OFTEN. Catching premature circularization can be easy in some cases, but very difficult in others.
April 28, 2025 at 8:08 AM
We observed cases of premature circularization. VERY OFTEN. Catching premature circularization can be easy in some cases, but very difficult in others.
We observed chimeric contigs where the assembly software reported a single contig that brought together sequences from two distinct taxa, sometimes three or more, and even sequences that belonged to distinct domains of life.
April 28, 2025 at 8:08 AM
We observed chimeric contigs where the assembly software reported a single contig that brought together sequences from two distinct taxa, sometimes three or more, and even sequences that belonged to distinct domains of life.
Unlike traditional evaluations of assembly software, our evaluation made quite a heavy use of unassembled long-reads to quantify how well the assembled sequences matched to long-reads. They generally worked great, but then sometimes they didn't at all. Here are a few things we observed:
April 28, 2025 at 8:08 AM
Unlike traditional evaluations of assembly software, our evaluation made quite a heavy use of unassembled long-reads to quantify how well the assembled sequences matched to long-reads. They generally worked great, but then sometimes they didn't at all. Here are a few things we observed:
But then we learned that Jill Banfield's group was dealing with similar issues in soil samples. At that point we decided to take a deeper look at our long-read assemblers, and used the datasets they used, and added some novel ones into the mix to re-evaluate them.
April 28, 2025 at 8:08 AM
But then we learned that Jill Banfield's group was dealing with similar issues in soil samples. At that point we decided to take a deeper look at our long-read assemblers, and used the datasets they used, and added some novel ones into the mix to re-evaluate them.
Our pangenomes were certainly raising some red flags. But we were not sure if fractions of genomes as circular elements were a feature of nature that we missed due to the years of short-read assemblies. With changing technology, you sometimes learn things you didn't even know you were missing.
April 28, 2025 at 8:08 AM
Our pangenomes were certainly raising some red flags. But we were not sure if fractions of genomes as circular elements were a feature of nature that we missed due to the years of short-read assemblies. With changing technology, you sometimes learn things you didn't even know you were missing.
While examining the assembly results we are initially extremely happy with the very large number of giant and occasionally circular contigs. Although we quickly realised that many of the circular contigs did not make any sense.
April 28, 2025 at 8:08 AM
While examining the assembly results we are initially extremely happy with the very large number of giant and occasionally circular contigs. Although we quickly realised that many of the circular contigs did not make any sense.
Assemblers play a significant role turning individual reads into long genomic segments, and have tremendous implications on downstream work. Last year we were very excited to apply some of the new assemblers to our PacBio datasets from marine samples.
April 28, 2025 at 8:08 AM
Assemblers play a significant role turning individual reads into long genomic segments, and have tremendous implications on downstream work. Last year we were very excited to apply some of the new assemblers to our PacBio datasets from marine samples.
With technologies such as PacBio and ONT, genome-resolved metagenomics is experiencing its second coming. Complete and circular genomes from all domains of life as well as viruses plasmids, all WITHOUT binning seem right around the corner. That is, if we can actually assemble them.
April 28, 2025 at 8:08 AM
With technologies such as PacBio and ONT, genome-resolved metagenomics is experiencing its second coming. Complete and circular genomes from all domains of life as well as viruses plasmids, all WITHOUT binning seem right around the corner. That is, if we can actually assemble them.