DRAM v1.3
DRAM v1.3 change log
- Add --amg_database_loc parameter that was missing in DRAM-setup.py
- Shift DRAM download of UniRef from FTP to HTTP address to address firewall issues
- Rename of headers in annotations.tsv files to be more uniform across databases
- By default
DRAM.py annotate
now does not annotated with VOGDB by default, flag added to use VOGDB - By default don't split
DRAM-v.py annotate
input contigs into separate files because HMMER doesn't care for E-values - Users can now pass multiple
--input_fasta
arguments toDRAM.py annotate
andDRAM-v.py annotate
- Now DRAM makes sure bin names (pulled from file names) are unique and not full paths
- Update pandas methods to get rid of warnings and increase speed
- When annotating with KEGG Genes the KEGG Genes IDs are stored in the
annotations.tsv
in addition to the KO IDs - Complete rewrite of how HMM annotation is handled inside DRAM to reduce redundancy and allow...
- Users can now annotate using custom HMM sets which may include custom bitScore cutoffs
- Complete rewrite of database handling from setup through annotation, in the future this will allow more flexible configuration
- Change CI to CircleCI from travis
- DRAM strainer and gene neighborhood pulling can now both use custom distillate information