Ragtag

Enhancements

This version contains an improvement to the assembly-to-assembly alignment merging algorithm.

Citation

Alonge, Michael, et al. ["RaGOO: fast and accurate reference-guided scaffolding of draft genomes."](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1829-6) Genome biology 20.1 (2019): 1-17.

Bug Fixes

- Minor bug fixes

Enhancements

NA

Citation

Alonge, Michael, et al. ["RaGOO: fast and accurate reference-guided scaffolding of draft genomes."](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1829-6) Genome biology 20.1 (2019): 1-17.

Bug Fixes

- Users are now warned when there are no useful assembly alignments

Enhancements

- Introduction of RagTag 'patch'

- More conservative assembly alignment merging

- Addition of .paf <-> .delta alignment conversion

- Support for the Unimap aligner for assembly-to-assembly alignment

- Addition of a utility for splitting assemblies at gaps

- Support for ONT data for correction validation

- Change of output file naming (formatted as `ragtag.<command>.*`)

Citation

Alonge, Michael, et al. ["RaGOO: fast and accurate reference-guided scaffolding of draft genomes."](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1829-6) Genome biology 20.1 (2019): 1-17.

Enhancements

- Added restriction sites for Arima 2.0

- Added a new assembly stats utility `ragtag.py asmstats`

Citation

Alonge, Michael, et al. ["RaGOO: fast and accurate reference-guided scaffolding of draft genomes."](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1829-6) Genome biology 20.1 (2019): 1-17.

Enhancements

- The beta version of a new utility, `ragtag.py merge`, is now available for merging AGP files. This adds `networkx` as a new dependency.

- Improved logging of internal scripts.

- The AGP file API is improved to organize objects, provide better error messages, and catch more AGP file format errors.

- Improved testing and UI.

Citation

Alonge, Michael, et al. ["RaGOO: fast and accurate reference-guided scaffolding of draft genomes."](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1829-6) Genome biology 20.1 (2019): 1-17.

Enhancements

- `ragtag_agp2fasta.py` can now handle portions of components, making it generic.

- Two new AGP utilities have been added: `agp2fasta` and `agpcheck`. The former generates AGP objects in fasta format given an AGP file and a components fasta file. The later performs most checks to ensure AGP file format validity.

Citation

Alonge, Michael, et al. ["RaGOO: fast and accurate reference-guided scaffolding of draft genomes."](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1829-6) Genome biology 20.1 (2019): 1-17.