Bioinformatics scientist @PacBio. I work on metagenomics, methylation, and assembly, but also enjoy phylogenomics and frog/lizard evolution. 🦠 🐸 🦎 🧬
Jan 12, 2023 • 8 tweets • 5 min read
Our updated study is published! We evaluated methods for taxonomic profiling and classification with long-read #metagenomic datasets. This included @PacBio and @nanopore data, and was a group effort with @saltyscientist and @ctitusbrown: bmcbioinformatics.biomedcentral.com/articles/10.11… 🧵1/8
Top performers include sourmash, @bugseq, and DIAMOND + MEGAN-LR, which displayed overall high precision and solid recall. We recommend trying all of these methods, and each has their own specific advantages. 2/8
Feb 2, 2022 • 8 tweets • 5 min read
What is the best method for taxonomic profiling in long-read shotgun #metagenomic datasets? We put several to the test in a new study, using @PacBio#HiFi and @nanopore data!!! Awesome collaboration with @ctitusbrown and @saltyscientist: biorxiv.org/content/10.110…. 🧵1/8
Top performers are long read methods including @bugseq and MEGAN-LR (using DIAMOND to NCBI nr), which had very high precision and solid recall (with no filtering necessary!). MMseqs2 and MetaMaps required some filtering to reduce false positives, but they also performed well. 2/8
