NAME

       iva - iterative virus assembler

DESCRIPTION

       usage: iva [options] {-f reads_fwd -r reads_rev | --fr reads} <output directory>

   positional arguments:
       Output directory
              Name of output directory (must not already exist)

   optional arguments:
       -h, --help
              show this help message and exit

   Input and output:
       -f filename[.gz], --reads_fwd filename[.gz]
              Name of forward reads fasta/q file. Must be used in conjunction with --reads_rev

       -r filename[.gz], --reads_rev filename[.gz]
              Name of reverse reads fasta/q file. Must be used in conjunction with --reads_fwd

       --fr filename[.gz]
              Name of interleaved fasta/q file

       --keep_files
              Keep  intermediate  files  (could  be  many!). Default is to delete all unnecessary
              files

       --contigs filename[.gz]
              Fasta file of contigs to be extended. Incompatible with --reference

       --reference filename[.gz]
              EXPERIMENTAL! This option is  EXPERIMENTAL,  not  recommended,  and  has  not  been
              tested!  Fasta file of reference genome, or parts thereof. IVA will try to assemble
              one contig per sequence in this file.  Incompatible with --contigs

       -v, --verbose
              Be verbose by printing messages to stdout. Use up to  three  times  for  increasing
              verbosity.

   SMALT mapping options:
       -k INT, --smalt_k INT
              kmer hash length in SMALT (the -k option in smalt index) [19]

       -s INT, --smalt_s INT
              kmer hash step size in SMALT (the -s option in smalt index) [11]

       -y FLOAT, --smalt_id FLOAT
              Minimum  identity threshold for mapping to be reported (the -y option in smalt map)
              [0.5]

   Contig options:
       --ctg_first_trim INT
              Number of bases to trim off the end of every contig before extending for the  first
              time [25]

       --ctg_iter_trim INT
              During  iterative  extension,  number of bases to trim off the end of a contig when
              extension fails (then try extending again) [10]

       --ext_min_cov INT
              Minimum kmer depth needed to use that kmer to extend a contig [10]

       --ext_min_ratio FLOAT
              Sets N, where kmer for extension must be at least N times more abundant  than  next
              most common kmer [4]

       --ext_max_bases INT
              Maximum number of bases to try to extend on each iteration [100]

       --ext_min_clip INT
              Set  minimum number of bases soft clipped off a read for those bases to be used for
              extension [3]

       --max_contigs INT
              Maximum number of contigs allowed in the assembly. No more seeds generated  if  the
              cutoff is reached [50]

   Seed generation options:
       --make_new_seeds
              When  no  more  contigs  can be extended, generate a new seed. This is forced to be
              true when --contigs is not used

       --seed_start_length INT
              When making a seed sequence, use the most common kmer of this length. Default is to
              use  the minimum of (median read length, 95). Warning: it is not recommended to set
              this higher than 95

       --seed_stop_length INT
              Stop extending seed using perfect matches from reads when this length  is  reached.
              Future extensions are then made by treating the seed as a contig [0.9*max_insert]

       --seed_min_kmer_cov INT
              Minimum kmer coverage of initial seed [25]

       --seed_max_kmer_cov INT
              Maximum kmer coverage of initial seed [1000000]

       --seed_ext_max_bases INT
              Maximum number of bases to try to extend on each iteration [50]

       --seed_overlap_length INT
              Number of overlapping bases needed between read and seed to use that read to extend
              [seed_start_length]

       --seed_ext_min_cov INT
              Minimum kmer depth needed to use that kmer to extend a contig [10]

       --seed_ext_min_ratio FLOAT
              Sets N, where kmer for extension must be at least N times more abundant  than  next
              most common kmer [4]

   Read trimming options:
       --trimmomatic FILENAME
              Provide  location  of  trimmomatic.jar  file  to  enable read trimming. Required if
              --adapters used

       --trimmo_qual STRING
              Trimmomatic  options  used  to   quality   trim   reads   [LEADING:10   TRAILING:10
              SLIDINGWINDOW:4:20]

       --adapters FILENAME
              Fasta  file  of  adapter  sequences to be trimmed off reads. If used, must also use
              --trimmomatic. Default is file of adapters supplied with IVA

       --min_trimmed_length INT
              Minimum length of read after trimming [50]

       --pcr_primers FILENAME
              FASTA file of primers. The first perfect match found to a sequence in  the  primers
              file  will be trimmed off the start of each read. This is run after trimmomatic (if
              --trimmomatic used)

   Other options:
       -i INT, --max_insert INT
              Maximum insert size (includes read length). Reads with inferred  insert  size  more
              than the maximum will not be used to extend contigs [800]

       -t INT, --threads INT
              Number of threads to use [1]

       --kmc_onethread
              Force  kmc  to  use  one  thread. By default the value of -t/--threads is used when
              running kmc

       --strand_bias FLOAT in [0,0.5]
              Set strand bias cutoff of mapped reads when trimming contig ends, in  the  interval
              [0,0.5].  A  value  of  x  means  that  a  base  needs  min(fwd_depth, rev_depth) /
              total_depth <= x. The only  time  this  should  be  used  is  with  libraries  with
              overlapping  reads (ie fragment length < 2*read length), and even then, it can make
              results worse. If used, try a low value like 0.1 first [0]

       --test Run using built in test data.  All  other  options  will  be  ignored,  except  the
              mandatory output directory, and --trimmomatic and --threads can be also be used

       --version
              show program's version number and exit