C. Titus Brown
C. Titus Brown
I wanted to write down some more thoughts on evaluation and contig-level stats. * it would be interesting to know which contigs currently filtered out by Reason 1 (gather matches...
[BlobToolKit – Interactive Quality Assessment of Genome Assemblies](https://www.g3journal.org/content/10/4/1361)
riffing off of [conterminator](https://github.com/martin-steinegger/conterminator), martin steinegger suggested that we look at using mmseqs2: > We have a method in MMseqs2 to predict a consensus taxonomical label for a contig by...
inspired by https://github.com/dib-lab/charcoal/issues/94, I'm not (yet) sure how to develop true confidence values, but we could certainly provide rankings. for example, * least confident tax identification - this would be...
GTDB 25k is all well and good, but probably not as sensitive as all of genbank. could we / should we build a "screened" genbank where we include any genome...
[DeepMAsED: evaluating the quality of metagenomic assemblies](https://academic.oup.com/bioinformatics/article-abstract/36/10/3011/5756210) Motivation Methodological advances in metagenome assembly are rapidly increasing in the number of published metagenome assemblies. However, identifying misassemblies is challenging due to...
[InStrain enables population genomic analysis from metagenomic data and rigorous detection of identical microbial strains](https://www.biorxiv.org/content/10.1101/2020.01.22.915579v1) Coexisting microbial cells of the same species often exhibit genetic differences that can affect phenotypes...
in theory, as we sequence more and more microbial genomes, charcoal should become better and better (balanced a bit by database size and the potential need to dereplicate through species...
[CheckV: assessing the quality of metagenome-assembled viral genomes](https://www.biorxiv.org/content/10.1101/2020.05.06.081778v1?rss=1) - not directly relevant, but perhaps inspirational reading