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." 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." 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." 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." 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." 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." Genome biology 20.1 (2019): 1-17.

Bug Fixes

• A bug associated with passing multiple read files is now fixed.

Enhancements

• -o is now a PATH type rather than a STR type. Any path can be provided with -o.

• There is now a better error message when the read alignment coverage information is not available.

• "Goodbye" is now logged at the end of execution to signal that ragtag has successfully completed.

• There is now new testing to test read validation with the -F option using E. coli data.

Citation

Alonge, Michael, et al. "RaGOO: fast and accurate reference-guided scaffolding of draft genomes." Genome biology 20.1 (2019): 1-17.

This release is the debut for RagTag, a reference-guided scaffolding tool that succeeds RaGOO.