RunMarkup
From ArachneWiki
| RunMarkup | |
|---|---|
| Function | Script |
| Phase | Analysis |
| Standard CLAs | PRE, DATA, RUN, SUBDIR, GDB, NO_HEADER |
| Special CLAs | TAG_REPEATS, BLESS, FULL_REPEATS, RUN_PAIRS, RUN_MARKUP, RUN_TRANSLATE, MAKE_READABLE, K |
| Source location | ARACHNE_DIR/qcmarkup |
RunMarkup is a script module that executes a number of other modules in order to collect information about an assembly. The pipeline includes:
- TagRepeats (if TAG_REPEATS=True) - for repeat finding
- PairAnnotator (if RUN_PAIRS=True) - for read pair analysis
- QualAnnotator
- HQDAnnotator
- RepeatAnnotator
- BlessContig, BlessAnnotator, BlessExternal (if BLESS=True)
- ClassifyDefects
- TranslateToPVals (if RUN_TRANSLATE=True) - uses a model to predict the presence of different kinds of assembly errors.
- DefectSummary (if RUN_TRANSLATE=True)
- ContigifyMarkup (if MAKE_READABLE=True)
- SafeGzip (if FULL_REPEATS=True)
A description of the RunMarkup output files and formats can be found in doc/AssemblyMarkup2.0.pdf (in the directory where you unpacked the source code).
