man iva (1): iterative virus assembler

DESCRIPTION

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

-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.

-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]

--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]

--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]

--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)

-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