Performs de novo clustering and consensus generation from full-length amplicon sequence reads, including raw PacBio and Oxford Nanopore data
Several common scientific computing packages for Python are required:
- matplotlib
- seaborn
- numpy
- scipy
- scikit-bio
The recommended method for building this environment is with Anaconda (or Miniconda):
conda create -n amp python=3.6 anaconda
conda activate amp
conda install -c https://conda.anaconda.org/biocore scikit-bio
python denovo_amp.py -h
usage: De novo clustering and consensus of long (full-length) amplicon sequences
[-h] [--verbosity VERBOSITY] [--start START] [--end END] fa ref aln out
positional arguments:
fa Read FASTA file
ref Initial consensus or ref FASTA
aln Initial consensus alignment (m5)
out Output prefix (incl. path)
optional arguments:
-h, --help show this help message and exit
--verbosity VERBOSITY
Level of output (0-3)
--start START Start position of ref to consider
--end END End position of ref to consider
blasr reads.fasta ref.fasta -m 5 -bestn 1 -out aln.m5
python denovo_amp.py read.fasta ref.fasta aln.m5 denovo_clusters