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