VirA: Viral Quasispecies Assembler (MaxBandwidth and AmpMCF tool)

VirA is a tool for assembling a viral quasispecies given an overlapping amplicon library.

VirA

Usage:

vira [-h] [-k FLOWS] [-m NUM_MISMATCH]
 [-n NUM_THREADS] [-t TIMEOUT] [-o OUTPUT_DIR]
 read_file ref_file primers

Positional arguments:

read_file:            Path to the FASTA file.

ref_file:             Reference sequence FASTA file.

primers:              FASTA file containing primers for each amplicon. Order
                      should be in amplicon coverage order: forward primer
                      then backward primer per amplicon.

Optional arguments:

-h, --help
  Show this help message and exit.

-k FLOWS, --flows FLOWS
  Number of commodities to use for MCF formulation.
  Default is 0, which indicates to use Max Bandwidth
  heuristic. Note: k > 0 requires CPLEX and CPLEX python
  module to be installed!

-m NUM_MISMATCH, --num_mismatch NUM_MISMATCH
  Number of allowed mismatches in read overlap. Default
  is 0.

-n NUM_THREADS, --num_threads NUM_THREADS
  Number of threads for CPLEX in MCF formulation.
  Default is total number of CPUs.

-t TIMEOUT, --timeout TIMEOUT
  Timeout in seconds until CPLEX must return an answer.
  This is used only when k > 0. Default is 600 seconds.

-o OUTPUT_DIR, --output_dir OUTPUT_DIR
  Directory to output the results. Default is current
  directory.

Examples

Running VirA on 454 data:

vira reads.fa ref.fa primers.fa

Try to reconstruct population of at most 25 haplotypes using multi-commodity flow formulation with a timeout after an hour (only includes reconstruction time, not alignment and error correction time):

vira -k 25 -t 3600 reads.fa ref.fa primers.fa