v0.6.0

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)

v0.5.7

• bug fix: computing of multiple PBC files from BAM or read data would only create one file thus creating duplicated coverage information
• slurm script now also globally accessible
• added dependency to setup of conda environment
• conda environment milts gets automatically activated and deactivated when running

v0.5.6

• updated handling of multiple coverage sets: paths are specified with numbers to make them distinguishable
• default values for config parameters: minimal require parameters has reduced to fasta_path, gff_path, output_path, taxon_id and database_path
• specific version requirements for R packages were dissolved
• 3D plots:
  • html file was made self-contained
  • title of html was changed to species name for easier handling of multiple plots
  • to accomodate newer versions of R packages, the html file is modified to keep text selectable
• MILTS can now be called from outside of its directory

v0.5.5

bug fixes

v0.5.4

added or changed headline of plot to species name
call MILTS.slurm either with path to config file or with option '-s/--seed' to specify a seedfile of config paths
-> sbatch MILTS.slurm -s seedfile.txt

v0.5.3

added possibility to select different source types in GFF for reading
new config parameter gff_source -> options:

• default (reads all gene, mRNA and CDS features)
• maker (reads gene and mRNA features from source 'maker', gene-protein linking via ID/Parent matching in mRNA feature)
• augustus_masked (reads match features from source 'augustus_masked', gene-protein linking via Name and ID attributes in match feature)
• path to parsing rule file (see information required in Wiki [coming soon])

reordering and renaming of some config parameters:

• tax_id -> taxon_id
• nr_db_path -> database_path
• only_plotting -> update_plots
• reads_1, reads_2, reads_un -> merged into 'reads' (see information on this in Wiki [coming soon])

v0.5.2

• stability fixes for NCBI taxon IDs missing with Taxopy package
• enhanced support of GFF formats

v0.5.1

minor bug fix

v0.5.0

updated taxonomic assignment process:

• LCA and best hit file are replaced by top 10% hit file
• runtime improvements for calculation of taxonomic assignments by using taxopy

automatic merging of taxonomic assignments to fit number of labels to be displayed

v0.4.2

size of ggplot output adjusted to legend size