dadaist2-dada2fasta

dadaist2-dada2fasta - a program to process the feature table generated by DADA2 (that uses the sequences as feature names) and saves it as feature table (using progressive feature names, or the MD5 of the sequences).

Author

Andrea Telatin andrea.telatin@quadram.ac.uk

Synopsis

dadaist2-dada2fasta  -i dada2table.tsv -o table.tsv -r repseqs.fasta

Parameters

Main Parameters

• -i, –input FILE

  Output produced by DADA2 (feature table tsv).

• -o, –output-table FILE

  Output feature table

• -r, –rep-seqs FILE

  Fasta output with the representative sequences.

• -s, –strip-pattern STR

  Remove from the sample names this string, usually found as filename suffix (default: _R1.fastq.gz)

• -p, –otu-prefix STR

  Prefix used for the represenative sequences, by default the MD5 of the sequence (example: ASV)

Source code and documentation

The program is freely available at https://quadram-institute-bioscience.github.io/dadaist2 released under the MIT licence. The website contains the full DOCUMENTATION and we recommend checking for updates.