Sequencing Fold Depth
Compute theoretical sequencing depth from individual read count, read length, and genome size.
Description
Theoretical sequencing depth divides total read bases by genome size.
Theoretical sequencing depth divides total read bases by genome size. It describes an average rather than the depth of every genomic position.
Compute theoretical sequencing depth from individual read count, read length, and genome size.
When to use Sequencing Fold Depth
Use this for the following task: Compute theoretical sequencing depth from individual read count, read length, and genome size.
Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
How to use Sequencing Fold Depth and understand its results
- Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
- Enter readCount, readLength, genomeBases using the field table, then run the tool.
- Read sequencedBases, foldCoverage. Interpret flags, units, ordering and placeholder values using the rules below.
- Review any reported issue or failed check, correct the supplied values when appropriate, and verify the result in its intended context.
| Input field | Meaning | Value type and bounds | Requirement |
|---|---|---|---|
| readCount | Individual reads, not read pairs. | integer; minimum 0 | Required |
| readLength | Read length | integer; minimum 1 | Required |
| genomeBases | Genome bases | integer; minimum 1 | Required |
Use nonnegative individual read count and positive read length/genome bases. Check the multiplied base count is a safe integer before dividing.1
sequencedBases = individualReadCount × readLength; foldCoverage = sequencedBases/genomeBases This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| sequencedBases | Sequenced bases | integer |
| foldCoverage | Fold coverage | number |
{
"input": {
"readCount": 100,
"readLength": 100,
"genomeBases": 1000
},
"output": {
"sequencedBases": 10000,
"foldCoverage": 10
}
}Limitations and assumptions
Count both mates as individual reads for paired sequencing. Mapping losses, overlapping mates and uneven coverage are not modeled.
The tool operates on supplied local data; alignment, filtering and annotation must already be appropriate for the stated calculation. Malformed requests produce input errors. A successfully evaluated request can still contain false flags, empty result lists or a result outside the supplied threshold; those outcomes have the meanings stated above.
Alternative or Complementary methods
Choose Target Coverage Read Pairs for this operation: Plan paired reads for target coverage from read length and usable on-target pair fraction. For a complementary task, use Poisson Uncovered Fraction for this operation: Estimate uncovered genome fraction under the uniform independent Poisson coverage model.
The implementation reference documents the exact calculation, supported input shapes and returned fields.
References
-
Sequencing Fold Depth — tool.io
Similar or alternative tools
- Target Coverage Read Pairs
Plan paired reads for target coverage from read length and usable on-target pair fraction.
- Poisson Uncovered Fraction
Estimate uncovered genome fraction under the uniform independent Poisson coverage model.