DNS
A DNS server is a computer that translates human-friendly domain names (like google.com) into numerical IP addresses that computers use to communicate.
DNS
A DNS server is a computer that translates human-friendly domain names (like google.com) into numerical IP addresses that computers use to communicate.
bluejay
BlueJ is a development environment that allows you to develop Java programs quickly and easily.
Install Conda via MambaForge
Bcz MambaForge is like Miniconda but optimized for speed. When you create complex environments like Bactopia's (dozens of tools!), mamba is significantly faster and more stable than conda.
Briefly, on request, empty bottles were shipped to worldwide project partners, who were briefed on sample inclusion criteria.
Crazy workload and connection
curated
Curated databases are databases that are populated and updated with a great deal of human effort.
BLASTn
Nucleotide BLAST, and it is a program used for aligning and comparing nucleotide (DNA or RNA) sequences. It's part of the larger Basic Local Alignment Search Tool (BLAST) suite of algorithms
protein homology models
Homology modeling is a computational method used to predict the 3D structure of a protein when its structure is not known, but the structure of a similar, homologous protein is.
HMMs
Hidden Markov Models (HMMs) are statistical models that analyze sequences (like protein or DNA sequences) to identify patterns and predict the likelihood of a sequence belonging to a certain class (e.g., an AMR gene).
Contig sequences were annotated as plasmidic using manual read tracking and four different software tools: PlasmidFinder with a minimum coverage of 75 % and the KMA mapping method (Carattoli et al., 2014); PlasForest v1.2 with a batch size of 500 (Pradier et al., 2021); Platon v1.7 in “accuracy” and “meta” modes (Schwengers et al., 2020); and PlasX using MMseqs v10.6 (Yu et al., 2024).
How to detect plasmidic contigs
For each sample, mapping rates were calculated concerning the total number of reads in that sample, both for all contig-mapping reads and specifically for those reads classified by Kraken2 to at least one species of the GTDB plasmids database, hereafter referred to as “GTDBp reads.”
To figure out the role of plasmid in microbial population
The USDA’s WGS protocol
Really good and comprehensive protocol
report of Kraken2
Please notice that the "Classification" one should be used instead of "Report"