Binning and Functional Annotation: Glossary

Key Points

Metagenome Binning

  • Metagenome-Assembled Genomes (MAGs) sometimes are obtained from curated contigs grouped into bins.

  • Use MetaBAT2 to assign the contigs to bins of different taxa.

  • Other programmes are available that are generating other bins, and these can be rationalised using tools such as DAStools
QC of metagenome bins

  • CheckM can be used to evaluate the quality of each Metagenomics-Assembled Genome.

  • We can use the percentage contamination and completion to identify the quality of these bins.

  • There are MIMAG standards which can be used to categorise the quality of a MAG.

  • Many MAGs will be incomplete, but that does not mean that this data is not still useful for downstream analysis.
Functional annotation

  • Functional annotation allows us to look at the metabolic capacity of a metagenome

  • Prokka can be used to predict genes in our assembly

  • Kofam scan can be used to identify KEGG IDs and enzyme numbers
Other Resources

  • Metagenomes are complicated to analyse. Luckily, there are lots of tools available!

  • The best tools to use change frequently. Do your research when looking for the most suitable tools to use for your analysis.

Glossary

accession
a unique identifier assigned to each sequence or set of sequences
categorical variable
Variables can be classified as categorical (aka, qualitative) or quantitative (aka, numerical). Categorical variables take on a fixed number of values that are names or labels.
cleaned data
data that has been manipulated post-collection to remove errors or inaccuracies, introduce desired formatting changes, or otherwise prepare the data for analysis
conditional formatting
formatting that is applied to a specific cell or range of cells depending on a set of criteria
CSV (comma separated values) format
a plain text file format in which values are separated by commas
factor
a variable that takes on a limited number of possible values (i.e. categorical data)
Gb
gigabyte of file storage or file size
Gbase
a gigabase represents one billion nucleic acid bases (Gbp may indicate one billion base pairs of nucleic acid)
headers
names at tops of columns that are descriptive about the column contents (sometimes optional)
metadata
data which describes other data
NGS
common acronym for “Next Generation Sequencing” currently being replaced by “High Throughput Sequencing”
null value
a value used to record observations missing from a dataset
observation
a single measurement or record of the object being recorded (e.g. the weight of a particular mouse)
plain text
unformatted text
quality assurance
any process which checks data for validity during entry
quality control
any process which removes problematic data from a dataset
raw data
data that has not been manipulated and represents actual recorded values
rich text
formatted text (e.g. text that appears bolded, colored or italicized)
string
a collection of characters (e.g. “thisisastring”)
TSV (tab separated values) format
a plain text file format in which values are separated by tabs
variable
a category of data being collected on the object being recorded (e.g. a mouse’s weight)