micca-otu-refΒΆ

micca-otu-ref builds the OTU table and performs the taxonomy assigment with the reference picking protocol. Reads are clustered against an external reference. Reads which do not hit a sequence in the reference are excluded.

$ micca-otu-ref --help
usage: micca-otu-ref [-h] [-v] [-M] [-f {fastq,fasta}] [-s SIMILARITY] --ref
                     FILE --ref-taxonomy FILE [-o DIR]
                     input [input ...]

micca-otu-ref builds the OTU table and performs the taxonomy assigment with the
reference picking protocol. Reads are clustered against an external reference. 
Reads which do not hit a sequence in the reference are excluded.

positional arguments:
  input                 input fastq/a file(s)

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit
  -M, --merged          the input file is a single fasta/q file where samples
                        were merged and the sequences ids are in the form
                        'SAMPLENAME||SEQID'
  -f {fastq,fasta}, --format {fastq,fasta}
                        input file format (default fastq)
  -s SIMILARITY, --similarity SIMILARITY
                        similarity between cluster center and cluster
                        sequences (default 0.97)
  --ref FILE            reference sequences in fasta format
  --ref-taxonomy FILE   tab-separated id-to-taxonomy file. First column
                        contains the sequence identifiers,and the second
                        column contains the taxonomy separated by semi-colons
                        (e.g., Bacteria;Firmicutes;Clostridia)
  -o DIR, --output-dir DIR
                        output directory (default .)

Example:

 $ micca-otu-ref sample*.fastq -s 0.97 --ref greengenes_2013_05/rep_set/97_otus.fasta \
   --ref-taxonomy greengenes_2013_05/taxonomy/97_otu_taxonomy.txt

micca v. 0.1.
Author: Davide Albanese <davide.albanese@fmach.it>
Fondazione Edmund Mach, 2014.

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