PROGRESS

$2022-01-17
Project created
$2023-11-23
Pipeline was moved to public repository in order to share with collaborators.
$2023-12-13
- blacklist is now called blocklist.
- The newly added uparse rule can take a few hours to run depending on data size.
- There is now more documentation in the code and in the readme.
- We added new options to the config file:
    - FORWARD_PRIMER_SEQUENCE: Forward primer sequences, in case you don't have a primers file (optional)
    - REVERSE_PRIMER_SEQUENCE: Reverse primer sequences, in case you don't have a primers file (optional)
    - allowUntrimmed: Option for --discard-untrimmed in cutadapt
    - runUSEARCH: Perform USEARCH sequence alignment and search for last common ancestor
    - runDefCom: Perform sequence alignment between Amplicon Sequence Variants and a reference sequence database of defined community members
    - REFERENCE_SEQUENCE_FILE: Reference sequence file of the defined community members (optional, only needed if you run runDefCom)