Connor Morgan-Lang
Connor Morgan-Lang
- [x] I checked and didn't found a related issue,e.g. while typing the title - [x] ** I got an error in the following rule(s):** `build_bin_report ` - [x] I...
Hi, I've been attempting to analyze a mock community assembly using metaquast, in quast 5.0.2, on a GCP VM. It failed after aligning the reads to the combined reference. I've...
Hi, I'm trying to run Metaquast on a mock community metagenome of 8 organims. The assembly and combined reference genomes are ~70Mbp each. I have 66Gb of uncompressed sequence reads...
Hi there, I've just started using PLASS, specifically `plass assemble`, and I really like it! This isn't an issue but a potential enhancement. I was wondering how I might be...
Taxonomic classification is reliant on the evolutionary distance (i.e. branch-length, or number of substitutions) linear model. Distances between query sequences and reference sequences inferred during phylogenetic placement are influenced by...
Use ClipKit instead of BMGE. Issue: #67
[ClipKIT](https://github.com/JLSteenwyk/ClipKIT) is a new MSA-trimming Python package. The authors indicate the trimmed MSAs generated by ClipKIT are more "desireable" (combined RF distance and bipartition supports) than those from competing tools,...
**Is your feature request related to a problem? Please describe.** A user, Aditi Nagaraj, found a series of ORFs predicted by Prodigal (within `treesapp assign`) that had fragmented a single...
`treesapp abundance` calculates TPM or FPKM for entire query sequences. The depth of coverage, however, is unknown. A new feature that reports the pile-up along each query sequence's length would...
`treesapp purity` is (mostly) good at indicating whether reference packages will end up classifying off-target homologs. A missing piece, however, leaves users unsure of what to do with the reference...