In preparation for the python package MILTS.sh was changed to milts.py
New features:
- taxonomic assignment is addable to GFF with script add_ta2gff.py (see instructions here)
- Mapping improvements: state read orientation and max + min insert size in config file (see Configuration parameters for options)
- added percentage of matches (pident) between query and best hit sequence to report and plot
- support of protein extraction based on special GFF sources (see details here)
- basic taxonomy summary: how many outside of query lineage and which superkingdom, kingdoms, phyla and classes are present
- number of threads used by Bowtie2 and DIAMOND can be adjusted in config file (see Configuration parameters for options)
Cosmetic updates:
- MILTS.slurm creates only one logfile
- removed coverage related info from output when not given
- rounded values in final output to two digits (except e-value and percentage of assembly length)
Bug fixes:
- partial genes are skipped and gene ID written to log
- matched index of coverage related parameters between config file and output
- symlink to protein fasta file is created in report directory (for GUI)