================================================================= 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] [-s {454,illumina,pacbio}] [-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. -s {454, illumina, pacbio}, --seq {454, illumina, pacbio} Technology used to produce the read data. Leave blank if tech used is not one of these three. Default is blank. -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: :command:`vira -s 454 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): :command:`vira -k 25 -t 3600 reads.fa ref.fa primers.fa` .. toctree:: :maxdepth: 2