Update README.md

[monica-cheng1]

Greptile Summary

The PR substantially expands the README with input requirements, specifications, use cases, FAQs, and citation details for MiXCR SHM Trees.

• SHM tree: A lineage representation of related B-cell sequences; changed from a short overview to a detailed explanation of observed and inferred nodes.
• Clonal family: Clonotypes grouped as a lineage within a donor; newly documented as the unit used for tree inference.
• MRCA: The most recent common ancestor of a branch; newly introduced to explain ancestral nodes and mutation-reference metrics.
• Sequence Search: A feature for locating nucleotide or amino-acid sequences in trees; newly documents targets, tolerance modes, mismatches, and indel handling.
• Basket: A named collection of selected tree nodes; newly defined along with its downstream-column behavior.
• Assembling feature: The sequence region used to assemble clonotypes; newly documents that inputs must be broader than CDR3, although the shared-feature requirement for combined datasets is omitted.
• Downsampling: Reduction of bulk datasets by reads, molecules, or clonotypes; newly added to the specifications.

Confidence Score: 4/5

The documentation-only PR appears safe to merge after addressing the omitted multi-dataset constraint and visible typo.

The implementation supports most newly documented capabilities, but combining datasets with different assembling features aborts the workflow despite the README presenting combination without that qualification.

Files Needing Attention: README.md

Important Files Changed

Filename	Overview
README.md	Expands user-facing product and workflow documentation, but omits a multi-dataset compatibility constraint and introduces a visible opening typo.

Prompt To Fix All With AI

### Issue 1
README.md:28
**Combined datasets require matching features**

The README says several datasets can be combined but omits that every dataset must use the same assembling feature; combining eligible datasets with different features causes the workflow to panic instead of producing trees.

```suggestion
* **Input:** a MiXCR clonotype dataset (`.clns`) from [MiXCR Clonotyping](https://github.com/platforma-open/mixcr-clonotyping), [MiXCR Amplicon Alignment](https://github.com/platforma-open/mixcr-amplicon-alignment), [MiXCR scFv Alignment](https://github.com/platforma-open/mixcr-scfv-clonotyping), or [Cellecta DriverMap AIR](https://github.com/platforma-open/cellecta-drivermap-air-mixcr-clonotyping) — bulk or single-cell BCR — assembled by a feature broader than CDR3, such as VDJRegion. A donor metadata column is also required, since trees are built within a donor. Several datasets can be combined under one donor column when they use the same assembling feature.
```

### Issue 2
README.md:15
**Opening word loses first letter**

The rewritten section begins with the visible typo “ithin” instead of “Within,” reducing the readability and polish of the README's opening explanation.

```suggestion
Within a B-cell clone, sequences are not independent observations — they are branches of a single evolutionary history. Somatic hypermutation and selection produce a family of related variants descending from one naive ancestor. Ranking those variants by abundance alone discards that structure.
```

---

For each issue above, determine whether it is valid and should be fixed. If so, fix it directly.

_{Reviews (1): Last reviewed commit: "Update README.md" | Re-trigger Greptile}

Greptile also left 1 inline comment on this PR.

[greptile-apps]

Combined datasets require matching features

The README says several datasets can be combined but omits that every dataset must use the same assembling feature; combining eligible datasets with different features causes the workflow to panic instead of producing trees.

Suggested change

* **Input:** a MiXCR clonotype dataset (`.clns`) from [MiXCR Clonotyping](https://github.com/platforma-open/mixcr-clonotyping), [MiXCR Amplicon Alignment](https://github.com/platforma-open/mixcr-amplicon-alignment), [MiXCR scFv Alignment](https://github.com/platforma-open/mixcr-scfv-clonotyping), or [Cellecta DriverMap AIR](https://github.com/platforma-open/cellecta-drivermap-air-mixcr-clonotyping) — bulk or single-cell BCR — assembled by a feature broader than CDR3, such as VDJRegion. A donor metadata column is also required, since trees are built within a donor. Several datasets can be combined under one donor column.

* **Input:** a MiXCR clonotype dataset (`.clns`) from [MiXCR Clonotyping](https://github.com/platforma-open/mixcr-clonotyping), [MiXCR Amplicon Alignment](https://github.com/platforma-open/mixcr-amplicon-alignment), [MiXCR scFv Alignment](https://github.com/platforma-open/mixcr-scfv-clonotyping), or [Cellecta DriverMap AIR](https://github.com/platforma-open/cellecta-drivermap-air-mixcr-clonotyping) — bulk or single-cell BCR — assembled by a feature broader than CDR3, such as VDJRegion. A donor metadata column is also required, since trees are built within a donor. Several datasets can be combined under one donor column when they use the same assembling feature.

Prompt To Fix With AI

This is a comment left during a code review.
Path: README.md
Line: 28

Comment:
**Combined datasets require matching features**

The README says several datasets can be combined but omits that every dataset must use the same assembling feature; combining eligible datasets with different features causes the workflow to panic instead of producing trees.

```suggestion
* **Input:** a MiXCR clonotype dataset (`.clns`) from [MiXCR Clonotyping](https://github.com/platforma-open/mixcr-clonotyping), [MiXCR Amplicon Alignment](https://github.com/platforma-open/mixcr-amplicon-alignment), [MiXCR scFv Alignment](https://github.com/platforma-open/mixcr-scfv-clonotyping), or [Cellecta DriverMap AIR](https://github.com/platforma-open/cellecta-drivermap-air-mixcr-clonotyping) — bulk or single-cell BCR — assembled by a feature broader than CDR3, such as VDJRegion. A donor metadata column is also required, since trees are built within a donor. Several datasets can be combined under one donor column when they use the same assembling feature.
```

---

For each issue above, determine whether it is valid and should be fixed. If so, fix it directly.