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Changelog.md

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1.3.6

  • Added config options for minimal merge length and full taxonomic levels
  • Count the number of reads at each step
  • Simplify the report and include table with read counts
  • Update Silva to 132
  • Fix conda environments for sina, report, itsx, cutadapt

1.3.5

  • Add LCA executable for filtering Blastn results
  • Add blast classification description to the report
  • Make more ouput files temporary
  • Fix issue with silva index files
  • Fix sina in report

1.3.4

  • Add ITSx to methods report
  • Add conda support for ITSx
  • Change from bbduk2.sh to bbduk.sh because it has been removed from the latest release

1.3.3

  • Allow renaming samples during configuration
  • Automatically replace underscores in sample names
  • Bugfixes:
    • rename classification method silva to sina
    • Fix merging pairs when not using barcode_in_header option

1.3.2

  • Bugfixes:
    • rdp confidence setting
    • add metadata to rdp and blast biom files
  • Report improvements:
    • UNITE citation
    • bbduk filtering
    • txt otutable download
    • otu fasta download

1.3.1

  • improved the automatic method template in the report
  • Allow more settings to be automatically defined in conf.py:
    • read stitching method
    • clustering
    • annotation
    • reference database
    • primers
  • minor bug fixes:
    • add conda config rdp
  • taxonomy formatting stampa
  • Download and reformat UNITE database for use with STAMPA

1.3

  • Allow for automatic configuration of remote projects at EBI.
  • Support for automatic testing using EBI data
  • Add config option to convert to Casava 1.8 format
  • Add step to filter PhiX reads and adapter traces
  • Add (optional) step to remove remaining barcodes from reads
  • Allow to process unidirectional (or only forward) sequences when using the mergepairs == none option
  • Support extraction and classification of ITS reads
  • Add 3 new method for taxonomy classification:
    • Add step to classify with pre-trained RDP database (for example UNITE for ITS)
    • Add STAMPA (vsearch) classification method
    • Add blast classification with lca option
  • Use conda to install Sina (with bugfix)
  • Add Swarm clustering method
  • Automatically download SILVA database for STAMPA and Sina and also trim the database with given primers for STAMPA
  • Improved generation of config file with conf.py
    • added command line options
    • automatically generate a metadata.txt template
  • Improved the report with a method part with references (bibtex)

1.2

  • Initial support for a report rule

1.1

  • Add support for automatically generated config files

1.0

  • First release