Glossary¶
| Term | Definition |
|---|---|
| ADD Accumulated Degree Days | A cumulative measure of temperature exposure over time. Used in this workshop as a continuous proxy for time since sample collection. |
| Alpha Diversity | Measurement of microbial diversity within a single sample. Includes richness, evenness, and sometimes phylogenetic relationships depending on the metric. |
| Alpha Correlation | Analysis testing relationships between alpha diversity metrics and continuous metadata variables. |
| ANCOM-BC Analysis of Compositions of Microbiomes with Bias Correction | A statistical method for identifying differentially abundant taxa between groups that accounts for the compositional nature of microbiome data. |
| Alpine Cluster | A high-performance computing (HPC) system used for running bioinformatics analyses. |
| Alpine OnDemand | A web portal interface used to access Alpine computing resources through a browser. |
| Amplicon | A DNA region amplified by PCR for sequencing, such as the V4 region of the 16S rRNA gene. |
| Barcode Index Sequence | A short DNA sequence added to a sample that uniquely identifies its reads during demultiplexing. |
| Barcoded PCR | A PCR strategy in which primers contain sample-specific barcode sequences. |
| Beta Diversity | Diversity between samples, describing how different microbial communities are from one another. |
| Categorical Variable | Metadata variable consisting of discrete groups (e.g., treatment or location). |
| Classifier | A trained machine-learning model that predicts taxonomy of unknown sequences using a reference database. |
| Chimera | A PCR artifact formed when fragments from multiple DNA templates combine into a single sequence. |
| Chimera Filtering | The process of detecting and removing chimeric sequences from a dataset. |
| Chloroplast Sequences | Plant-derived sequences that appear in 16S datasets because chloroplasts evolved from cyanobacteria. |
| Compressed Sequencing Files .fastq.gz | Raw sequencing data files compressed using gzip to reduce storage requirements. |
| Compute Node | A non-interactive computing resource where submitted jobs are executed. |
| Continuous Variable | A numeric metadata variable with a range of values (e.g., temperature or time). |
| DADA2 Divisive Amplicon Denoising Algorithm 2 | A bioinformatics method that models sequencing errors to infer true biological sequences (ASVs) from amplicon data. |
| Demultiplexing Demux | The process of separating pooled sequencing reads into individual samples using barcode sequences. |
| Denoising | The process of correcting sequencing errors, removing artifacts, and generating ASVs from raw sequencing reads. |
| Diversity Metric | Any quantitative measure describing microbial diversity within or between samples. |
| Faith's PD Faith's Phylogenetic Diversity | The total branch length of a phylogenetic tree spanning taxa in a sample; incorporates evolutionary relationships. |
| FASTQ File | A sequencing file format storing DNA sequences and their quality scores. |
| Feature Table | A matrix of samples × features (ASVs or taxa) containing counts or frequencies. |
| GreenGenes2 GG2 | A curated 16S rRNA reference database used for taxonomic classification and phylogenetic placement. |
| Importing | The process of converting raw sequencing data into QIIME 2 artifacts (.qza files). |
| Interactive Node | A computing session where commands are run interactively (e.g., via sinteractive). |
| Job Script | A shell script submitted to a cluster containing resource requests and commands for execution. |
| Kruskal–Wallis Test | A nonparametric statistical test used to determine whether differences exist between two or more groups. |
| LME Linear Mixed Effects Model | A statistical model that accounts for both fixed and random effects in longitudinal or repeated-measures data. |
| Manifest File | A file mapping sample IDs to FASTQ file paths for QIIME 2 import. |
| Mitochondrial Sequences | Eukaryotic-derived sequences appearing in 16S datasets due to bacterial evolutionary origin of mitochondria. |
| Multiplexing | The pooling of multiple samples in one sequencing run to reduce cost. |
| Naive Bayes Classifier | A machine learning algorithm used for taxonomic classification of sequences based on a reference database. |
| OTU Operational Taxonomic Unit | A cluster of sequences grouped by similarity (typically 97% identity); largely replaced by ASVs. |
| Paired-End Reads | Sequencing reads generated from both ends of a DNA fragment. |
| Partition | A queue of compute resources with specific hardware and usage policies in SLURM. |
| PCoA Principal Coordinates Analysis | An ordination method that visualizes similarities/differences between samples based on distance matrices. |
| PERMANOVA Permutational Multivariate Analysis of Variance | A statistical test for differences in community composition using distance matrices. |
| Phred Score Q Score | A measure of sequencing accuracy (e.g., Q30 = 99.9% accuracy). |
| Pielou's Evenness | A measure of how evenly taxa are distributed within a sample. |
| Phylogenetic Diversity | Diversity metric that incorporates evolutionary relationships between taxa. |
| QIIME 2 | An open-source microbiome bioinformatics platform for analyzing amplicon sequencing data. |
| Quality Filtering | Removal of low-quality reads or bases based on quality scores. |
| QZA / QZV | QIIME 2 artifact (.qza) and visualization (.qzv) file formats. |
| Rarefaction | Subsampling reads to equal sequencing depth across samples. |
| Rarefaction Curve | A plot showing how observed diversity changes with sequencing depth. |
| Reference Database | A curated collection of sequences with known taxonomy used for classification (e.g., GreenGenes2). |
| Relative Abundance | The proportion of reads assigned to a taxon relative to total reads in a sample. |
| Read Merging | Combining overlapping forward and reverse reads into a single sequence. |
| Representative Sequences | The sequence representing each ASV after denoising. |
| Richness | The number of unique taxa present in a sample. |
| sbatch | The SLURM command used to submit jobs to a cluster queue. |
| SEPP SATe-enabled Phylogenetic Placement | A method for placing sequences into a reference phylogenetic tree. |
| Shannon Entropy | A diversity metric that accounts for both richness and evenness. |
| Shebang #!/bin/bash | The first line of a shell script defining the interpreter. |
| Single-End Reads | Sequencing reads generated from one end of a DNA fragment. |
| SLURM Simple Linux Utility for Resource Management | A workload manager used to schedule jobs on HPC systems. |
| Saturation of the Rarefaction Curve | Point where additional sequencing depth no longer increases observed diversity. |
| Taxa Bar Plot | A stacked bar plot showing relative abundance of microbial taxa across samples. |
| Taxa Filtering | Removal of unwanted taxa (e.g., plant or host DNA) from datasets. |
| Taxonomic Classification | Assignment of taxonomy to sequences using a reference database. |
| Taxonomy | The hierarchical classification system for organisms (kingdom → species). |
| Trim Left --p-trim-left | Removes bases from the start of sequencing reads. |
| Truncation --p-trunc-len | Trims reads to a fixed length from the end. |
| UniFrac | A phylogenetic beta diversity metric based on shared branch lengths between samples. |