/amplicon_cluster

De novo clustering of full-length amplicon sequences

Primary LanguagePython

Amplicon Clustering

Performs de novo clustering and consensus generation from full-length amplicon sequence reads, including raw PacBio and Oxford Nanopore data

Installation

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

Usage

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

Example

blasr reads.fasta ref.fasta  -m 5 -bestn 1 -out aln.m5
python denovo_amp.py read.fasta ref.fasta aln.m5 denovo_clusters