Changes in version 3.19                         

Bug Fixes

  - Identified the Rbowtie2 parameter k as being doubled when specified
    for bowtie filter or align steps.
  - Added another call to taxize in convert_animalcules() to catch any
    accessions that were not mapped to a UID in metascope_id(), in
    addition to another call in metascope_id() itself

Major changes

  - Altered bt2_params objects to reflect 98% identity (16S), 95%
    identity (metagenomics) and added a parameter for when the origin
    genome is thought to not be present in the reference database.
  - Added SILVA species_headers object called internally in
    convert_animalcules_silva
  - Added convert_animalcules_silva function

                        Changes in version 3.18                         

Bug Fixes

  - Fixed taxonomy table function to output correctly formatted table
  - Fixed examples for various functions that were calling genomes with
    download_refseq but genomes were not able to be found.
  - Fixed plot generation for metascope_id()
  - Fixed premature stopping of download_refseq for strains labeled as
    "no rank" in NCBI.
  - Fixed identification of reads as unknown genomes (due to outdated
    reference databases that identify genomes now removed from NCBI).
    The unknown genomes will now be distinctly identified based on NCBI
    accession ID, which will separate them in the final results. IDs can
    also be looked up manually (on NCBI website) to see what the reads
    were aligning to.
  - Incorporated unknown taxa (removed from NCBI databases) into output
    of convert_animalcules()

Major changes

  - Added ability to identify reads from databases other than NCBI
    (known to work for Silva and Greengenes2)

                       Changes in version 0.99.0                        

  - Pre-Release version of MetaScope

Bug Fixes

  - Fixed check error message about data.table::fread for reading .gz
    files by adding R.utils to imports.

Major Changes

  - Submitted to Bioconductor

Minor Changes