Field guide · reference
Glossary
Plain definitions of the terms used across genome curation and the OpenPretext contact map, from contigs and scaffolds to compartments and AGP. New to curation? Start with the field guide, or read the analysis page for the deeper measurements.
Assembly and curation
The assembly and its errors
- Assembly
- The set of sequences a genome project produces from its sequencing reads. A draft assembly, before curation, usually contains ordering and orientation errors.
- Contig
- A stretch of sequence assembled from overlapping reads, with no gaps inside it.
- Scaffold
- One or more contigs placed in order and orientation, with gaps of estimated length between them. Curation groups contigs into chromosome-scale scaffolds.
- Curation
- Correcting an assembly by hand, adjusting the order, orientation, and joins of its contigs, usually guided by a Hi-C contact map.
- Misassembly
- A placement error made by the assembler: a wrong join, a piece in the wrong orientation, or two unrelated regions fused into one contig.
- Chimera
- A single contig the assembler built from two unrelated regions. The signal drops sharply in the middle of the block; the fix is to cut it at the break.
- Inversion
- A stretch of sequence assembled in the wrong orientation. On the map it breaks and crosses the diagonal; the fix is to flip it.
- Translocation
- Sequence joined to the wrong location, often the wrong chromosome. On the map it appears as a bright block far off the diagonal.
- Haplotype
- One of the two sequence copies of a chromosome in a diploid organism, one inherited from each parent.
- Haplotig
- A contig representing the alternate haplotype of a region already present in the primary assembly, so that region is represented twice. Confirmed haplotigs are tagged out of the primary set. See coverage.
The contact map
Reading the map and its data
- Hi-C
- A sequencing method that records how often two pieces of DNA are close together in the nucleus. Nearby sequences produce more contacts.
- Contact map
- A square matrix of contact frequencies between genomic positions. Brighter cells mean more contacts. It is the main view in OpenPretext.
- Diagonal
- The line down the middle of the map where each position meets itself. It is always the strongest signal and the baseline for reading the rest.
- .pretext
- The binary contact-map file OpenPretext reads, produced by PretextMap. It stores the map as a multi-resolution image, so the overview loads without the full data.
- Coverage
- How many sequencing reads span a position, also called read depth. A retained haplotig sits near half the assembly's coverage.
Contiguity metrics
Measuring the assembly
- N50
- The length at which half of the assembly is contained in pieces at least that long. Contig N50 measures the raw assembly; scaffold N50 rises as contigs are grouped into chromosomes.
- auN
- A length-weighted average of piece length. It responds to change more smoothly than N50, because every piece contributes in proportion to its length.
- Health score
- OpenPretext's summary of assembly quality from 0 to 100, combining contiguity, contact decay, integrity, compartment strength, and library quality.
- QV
- A measure of per-base accuracy on a log scale, where Q40 is one error in 10,000 bases. Measuring it needs the sequencing reads, so a contact map alone cannot report it.
Structure analysis
The deeper measurements
These come from the 3D Analysis panel and are explained in full, with interactive figures, on the analysis page.
- Contact decay, P(s)
- How contact frequency falls as two positions move apart along a chromosome. Its slope on a log-log plot reflects how tightly the genome is packed.
- A/B compartments
- The division of chromatin into an active, gene-rich A compartment and a quiet, dense B compartment. On the map they form a checkerboard.
- Saddle plot
- A single-square summary of compartment strength, made by sorting bins from most B to most A and averaging their contacts.
- Insulation and TAD boundaries
- Insulation dips where a region is walled off from its neighbors. The deepest dips mark boundaries between chromosome neighborhoods.
- Observed over expected, O/E
- The contact map divided by the average contact at each genomic distance. Removing the distance decay makes long-range structure, such as compartments, visible.
- Virtual 4C
- The contact profile of a single chosen locus across the whole genome, the way a 4C experiment would measure it.
Biology to recognize
Real features, not errors
These make unusual shapes on the map but are real biology. See telling biology from error in the field guide.
- Centromere
- The repeat-rich region where a chromosome attaches to the spindle during division. On the map it shows as a faint band, not a break, and should not be cut.
- Telomere
- The repetitive sequence that caps a chromosome end.
- Satellite DNA and repeats
- Highly repetitive sequence that maps to more than one place, producing dense or off-diagonal signal that can resemble a misassembly.
- rDNA
- Tandem arrays of the ribosomal RNA genes, another repeat-rich region that can look unusual on the map.
- Sex chromosome
- A chromosome that differs between the sexes, such as X and Y in mammals or Z and W in birds. A degenerate W or Y is gene-poor and gives a faint, sparse block.
- Karyotype
- The number and appearance of a species' chromosomes. Knowing it helps decide how many scaffolds a finished assembly should have.
File formats
Getting data in and out
- FASTA
- A plain text format for sequence. OpenPretext exports the curated assembly as FASTA, reverse-complementing any inverted contigs.
- AGP
- A tab-delimited format that records how contigs are ordered and oriented into scaffolds. OpenPretext both imports and exports AGP.
- BED
- A format for genomic intervals. OpenPretext can export feature coordinates as BED.
- BedGraph
- A format for per-position values such as coverage. PretextGraph can embed BedGraph data into a .pretext file as an annotation track.
Keep going
Read the map with these in hand
The field guide puts these terms to work, from reading a contact map to finishing an assembly.