Target Coverage Read Pairs
Plan paired reads for target coverage from read length and usable on-target pair fraction.
Description
Paired-read planning combines two read lengths per pair with a usable on-target fraction.
Paired-read planning combines two read lengths per pair with a usable on-target fraction. Rounding upward ensures the planned number reaches the requested theoretical depth.
Plan paired reads for target coverage from read length and usable on-target pair fraction.
When to use Target Coverage Read Pairs
Use this for the following task: Plan paired reads for target coverage from read length and usable on-target pair fraction.
Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
How to use Target Coverage Read Pairs 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 targetBases, targetDepth, readLength, usablePairFraction using the field table, then run the tool.
- Read requiredReadPairs, requiredRawReadBases. 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 |
|---|---|---|---|
| targetBases | Target bases | integer; minimum 1 | Required |
| targetDepth | Target depth | number; greater than 0 | Required |
| readLength | Read length | integer; minimum 1 | Required |
| usablePairFraction | Usable on-target fraction of read pairs in (0, 1]. | number; greater than 0; maximum 1 | Required |
Require positive target/read lengths and depth and a usable fraction in (0,1]. Compute the ceiling from exact binary-number components and return raw bases as pairs × 2 × readLength.1
pairs = ceil(targetBases × targetDepth/(2 readLength usablePairFraction)) This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| requiredReadPairs | Required read pairs | integer |
| requiredRawReadBases | Required raw read bases | integer |
{
"input": {
"targetBases": 1000,
"targetDepth": 20,
"readLength": 100,
"usablePairFraction": 0.5
},
"output": {
"requiredReadPairs": 200,
"requiredRawReadBases": 40000
}
}Limitations and assumptions
Uniform usable coverage is assumed. Safe-count overflow is rejected; duplicates, overlap and assay losses must be reflected in the usable fraction.
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 Sequencing Fold Depth for this operation: Compute theoretical sequencing depth from individual read count, read length, and genome size. For a complementary task, use On Target Read Efficiency for this operation: Compute capture efficiency as the fraction of mapped reads overlapping targets.
The implementation reference documents the exact calculation, supported input shapes and returned fields.
References
-
Target Coverage Read Pairs — tool.io
Similar or alternative tools
- Sequencing Fold Depth
Compute theoretical sequencing depth from individual read count, read length, and genome size.
- On Target Read Efficiency
Compute capture efficiency as the fraction of mapped reads overlapping targets.