Last time I described a way to search MAGs in metagenomes, and teased about interesting results. Let's dig in some of them! I prepared a repo with the data and a notebook with the analysis I did in this post. You can also follow along in Bi…
(or: Top-down and bottom-up approaches for working around sourmash limitations) In the last month I updated wort, the system I developed for computing sourmash signature for public genomic databases, and started calculating signatures for t…
sourmash 3.3 was released last week, and it is the first version supporting zipped databases. Here is my personal account of how that came to be =] A sourmash database contains signatures (typically Scaled MinHash sketches built from genomi…
sourmash 3 was released last week, finally landing the Rust backend. But, what changes when developing new features in sourmash? I was thinking about how to best document this process, and since PR #826 is a short example touching all the l…
In January I wrote a post for the Rust 2019 call for blogs. The 2020 call is aiming for an RFC and roadmap earlier this time, so here is my 2020 post =] This sort of happened... because WebAssembly is growing =] I was very excited when Inte…
The Rust community requested feedback last year for where the language should go in 2018, and now they are running it again for 2019. Last year I was too new in Rust to organize a blog post, but after an year using it I feel more comfortabl…
sourmash calculates MinHash signatures for genomic datasets, meaning we are reducing the data (via subsampling) to a small representative subset (a signature) capable of answering one question: how similar is this dataset to another one? Th…
I think the first time I heard about Rust was because Frank Mcsherry chose it to write a timely dataflow implementation. Since then it started showing more and more in my news sources, leading to Armin Ronacher publishing a post in the Sent…
With the MinHash craze currently going on in the lab, we started discussing how to calculate signatures efficiently, how to index them for search and also how to distribute them. As a proof of concept I started implementing a system to read…
Since last month I'm a PhD student in MSU at Titus lab, and my research is focused on building infrastructure for exploring and merging multiple read types and multiples assemblies. Titus and all the labbies are awesome mentors, and I'm mak…
Last weekend I went with some friends to Maracanã watch Italy vs Mexico at the first round of the Confederations Cup. We got some cheap tickets (R$ 57, about US$ 25) on an area meant for Brazilians only (and that's why they were so cheap, u…
Blog juntando moscas, deixa eu ressucitar um projetinho de fim de semana para ver se anima um pouco. A ideia inicial desse post surgiu na PythonBrasil do ano passado. Pensei em fazer uma lightning talk, mas não ficou pronta a tempo (Nota: s…