Ben J Woodcroft
@benjwoodcroft.bsky.social
Yet another microbial bioinformatician, group leader, dad
github.com/wwood https://research.qut.edu.au/cmr/team/ben-woodcroft/
github.com/wwood https://research.qut.edu.au/cmr/team/ben-woodcroft/
@ace-gtdb.bsky.social R226-based profiles from 700k public metagenomes are at sandpiper.qut.edu.au. Search for your fave microbe by GTDB taxonomy there and see to get prevalence and community profiles. Got something novel? Get in touch.
July 16, 2025 at 9:59 PM
@ace-gtdb.bsky.social R226-based profiles from 700k public metagenomes are at sandpiper.qut.edu.au. Search for your fave microbe by GTDB taxonomy there and see to get prevalence and community profiles. Got something novel? Get in touch.
Fast and RAM-efficient since most raw reads are swiftly ignored. We optimise an up-front DIAMOND BLASTX-based method. Thanks @bbuchfink.bsky.social / Serratus for makeidx
July 16, 2025 at 9:59 PM
Fast and RAM-efficient since most raw reads are swiftly ignored. We optimise an up-front DIAMOND BLASTX-based method. Thanks @bbuchfink.bsky.social / Serratus for makeidx
Perhaps most strikingly, it detects microbes that aren't in the ref db, correctly weighting their relative abundance.
July 16, 2025 at 9:59 PM
Perhaps most strikingly, it detects microbes that aren't in the ref db, correctly weighting their relative abundance.
It's accurate on communities of known species / non-rep strains (though can struggle with low abundance species where coverage <1X)
July 16, 2025 at 9:59 PM
It's accurate on communities of known species / non-rep strains (though can struggle with low abundance species where coverage <1X)
SingleM is a new approach to metagenome profiling. It uses conserved regions within marker genes (20aa) spanned by individual short reads. Concentrating analysis on these regions makes things easier.
July 16, 2025 at 9:59 PM
SingleM is a new approach to metagenome profiling. It uses conserved regions within marker genes (20aa) spanned by individual short reads. Concentrating analysis on these regions makes things easier.
In environmental samples 75% lack a genome/MAG (abundance-weighted). We aren't near to a genome for all species, not even close.
July 16, 2025 at 9:59 PM
In environmental samples 75% lack a genome/MAG (abundance-weighted). We aren't near to a genome for all species, not even close.
Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵
July 16, 2025 at 9:59 PM
Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵
@rossenzhao.bsky.social's shiny new phage profiling tool for finding (novel) phage in metagenome reads a la SingleM. New SingleM release also brings @ace-gtdb.bsky.social R226. Manuscript is draft, but working code is here pre-pre-publication. Feedback most welcome.
May 16, 2025 at 12:04 PM
@rossenzhao.bsky.social's shiny new phage profiling tool for finding (novel) phage in metagenome reads a la SingleM. New SingleM release also brings @ace-gtdb.bsky.social R226. Manuscript is draft, but working code is here pre-pre-publication. Feedback most welcome.
A 1.0 release for Sandpiper. 700,000 microbial community profiles (3x the last version, 4.7 Pbp metaG), searchable via the @ace-gtdb.bsky.social R226 taxonomy that just dropped. MetaGs are going exponential, but we are still nowhere near a MAG for all species. sandpiper.qut.edu.au #microsky 🧬🖥️ 1/2
April 17, 2025 at 11:06 AM
A 1.0 release for Sandpiper. 700,000 microbial community profiles (3x the last version, 4.7 Pbp metaG), searchable via the @ace-gtdb.bsky.social R226 taxonomy that just dropped. MetaGs are going exponential, but we are still nowhere near a MAG for all species. sandpiper.qut.edu.au #microsky 🧬🖥️ 1/2
Wrapt for @iambrettb.bsky.social winning the student prize at @mgeaus.bsky.social - "Estimation of phage species trees using gene/species tree reconciliation". Hoping we can have an impact on viral phylogeny with these new methods, carefully applied.
February 18, 2025 at 6:07 AM
Wrapt for @iambrettb.bsky.social winning the student prize at @mgeaus.bsky.social - "Estimation of phage species trees using gene/species tree reconciliation". Hoping we can have an impact on viral phylogeny with these new methods, carefully applied.