topic: align
19 modules sharing the align name family (derived from the tree's prefix discipline).
The 'align' topic family in the Nishi sovereign ecosystem provides tools for sequence alignment and related operations, supporting both local and affine gap models. Modules like nx_align and nx_align_affine implement the Smith-Waterman algorithm with different gap penalties, while nx_align_backtrace generates CIGAR strings for alignment results. Additional modules handle chain-based alignment strategies, such as nx_align_chain, enabling efficient alignment of large datasets through dynamic programming.
auto-narrated by the local model from this topic's module headers; links verified against the wiki index.
narrated overview -- maintained by the narration lane, module links verified against this wiki.
| module | description | lines | funcs |
|---|---|---|---|
| nx_align.nx | Smith-Waterman local alignment, linear-gap. | 164 | 3 |
| nx_align_affine.nx | Smith-Waterman local alignment, AFFINE gap. | 199 | 2 |
| nx_align_affine_test.nx | KAT for Gotoh 1982 affine-gap SW. | 139 | 1 |
| nx_align_backtrace.nx | Smith-Waterman backtrace with CIGAR output. | 474 | 2 |
| nx_align_backtrace_test.nx | KAT for SW backtrace + CIGAR ops. | 209 | 1 |
| nx_align_chain.nx | co-linear seed-chain dynamic programming. | 153 | 1 |
| nx_align_chain_stranded.nx | strand-partitioned co-linear chain DP. | 162 | 1 |
| nx_align_chain_stranded_test.nx | KAT for strand-partitioned chain. | 136 | 1 |
| nx_align_chain_test.nx | KAT for the co-linear seed-chain DP. | 161 | 1 |
| nx_align_gate.nx | VERDICT gate for flexbox align-items (cross-axis alignment). A 100px-tall flex row | 142 | 7 |
| nx_align_match.nx | minimizer-based seed match (query vs reference). | 215 | 4 |
| nx_align_match_stranded.nx | strand-aware seed matcher. | 144 | 1 |
| nx_align_match_stranded_test.nx | KAT for strand-aware seed matcher. | 173 | 1 |
| nx_align_match_test.nx | end-to-end seed-pipeline KAT. | 251 | 1 |
| nx_align_minimizer.nx | canonical k-mer minimizer extraction. | 154 | 2 |
| nx_align_minimizer_test.nx | KAT for minimizer extraction. | 135 | 1 |
| nx_align_score.nx | score chained alignment via Smith-Waterman. | 153 | 2 |
| nx_align_score_test.nx | end-to-end seed-and-extend pipeline KAT. | 185 | 1 |
| nx_align_test.nx | KAT for Smith-Waterman local alignment. | 156 | 2 |