.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH IVA "1" "February 2024" "iva 1.0.8" "User Commands"
.SH NAME
iva \- iterative virus assembler
.SH DESCRIPTION
usage: iva [options] {\-f reads_fwd \fB\-r\fR reads_rev | \fB\-\-fr\fR reads} <output directory>
.SS "positional arguments:"
.TP
Output directory
Name of output directory (must not already exist)
.SS "options:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.SS "Input and output:"
.TP
\fB\-f\fR filename[.gz], \fB\-\-reads_fwd\fR filename[.gz]
Name of forward reads fasta/q file. Must be used in
conjunction with \fB\-\-reads_rev\fR
.TP
\fB\-r\fR filename[.gz], \fB\-\-reads_rev\fR filename[.gz]
Name of reverse reads fasta/q file. Must be used in
conjunction with \fB\-\-reads_fwd\fR
.TP
\fB\-\-fr\fR filename[.gz]
Name of interleaved fasta/q file
.TP
\fB\-\-keep_files\fR
Keep intermediate files (could be many!). Default is
to delete all unnecessary files
.TP
\fB\-\-contigs\fR filename[.gz]
Fasta file of contigs to be extended. Incompatible
with \fB\-\-reference\fR
.TP
\fB\-\-reference\fR 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 \fB\-\-contigs\fR
.TP
\fB\-v\fR, \fB\-\-verbose\fR
Be verbose by printing messages to stdout. Use up to
three times for increasing verbosity.
.SS "SMALT mapping options:"
.TP
\fB\-k\fR INT, \fB\-\-smalt_k\fR INT
kmer hash length in SMALT (the \fB\-k\fR option in smalt
index) [19]
.TP
\fB\-s\fR INT, \fB\-\-smalt_s\fR INT
kmer hash step size in SMALT (the \fB\-s\fR option in smalt
index) [11]
.TP
\fB\-y\fR FLOAT, \fB\-\-smalt_id\fR FLOAT
Minimum identity threshold for mapping to be reported
(the \fB\-y\fR option in smalt map) [0.5]
.SS "Contig options:"
.TP
\fB\-\-ctg_first_trim\fR INT
Number of bases to trim off the end of every contig
before extending for the first time [25]
.TP
\fB\-\-ctg_iter_trim\fR INT
During iterative extension, number of bases to trim
off the end of a contig when extension fails (then try
extending again) [10]
.TP
\fB\-\-ext_min_cov\fR INT
Minimum kmer depth needed to use that kmer to extend a
contig [10]
.TP
\fB\-\-ext_min_ratio\fR FLOAT
Sets N, where kmer for extension must be at least N
times more abundant than next most common kmer [4]
.TP
\fB\-\-ext_max_bases\fR INT
Maximum number of bases to try to extend on each
iteration [100]
.TP
\fB\-\-ext_min_clip\fR INT
Set minimum number of bases soft clipped off a read
for those bases to be used for extension [3]
.TP
\fB\-\-max_contigs\fR INT
Maximum number of contigs allowed in the assembly. No
more seeds generated if the cutoff is reached [50]
.SS "Seed generation options:"
.TP
\fB\-\-make_new_seeds\fR
When no more contigs can be extended, generate a new
seed. This is forced to be true when \fB\-\-contigs\fR is not
used
.TP
\fB\-\-seed_start_length\fR 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
.TP
\fB\-\-seed_stop_length\fR 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]
.TP
\fB\-\-seed_min_kmer_cov\fR INT
Minimum kmer coverage of initial seed [25]
.TP
\fB\-\-seed_max_kmer_cov\fR INT
Maximum kmer coverage of initial seed [1000000]
.TP
\fB\-\-seed_ext_max_bases\fR INT
Maximum number of bases to try to extend on each
iteration [50]
.TP
\fB\-\-seed_overlap_length\fR INT
Number of overlapping bases needed between read and
seed to use that read to extend [seed_start_length]
.TP
\fB\-\-seed_ext_min_cov\fR INT
Minimum kmer depth needed to use that kmer to extend a
contig [10]
.TP
\fB\-\-seed_ext_min_ratio\fR FLOAT
Sets N, where kmer for extension must be at least N
times more abundant than next most common kmer [4]
.SS "Read trimming options:"
.TP
\fB\-\-trimmomatic\fR FILENAME
Provide location of trimmomatic.jar file to enable
read trimming. Required if \fB\-\-adapters\fR used
.TP
\fB\-\-trimmo_qual\fR STRING
Trimmomatic options used to quality trim reads
[LEADING:10 TRAILING:10 SLIDINGWINDOW:4:20]
.TP
\fB\-\-adapters\fR FILENAME
Fasta file of adapter sequences to be trimmed off
reads. If used, must also use \fB\-\-trimmomatic\fR. Default
is file of adapters supplied with IVA
.TP
\fB\-\-min_trimmed_length\fR INT
Minimum length of read after trimming [50]
.TP
\fB\-\-pcr_primers\fR 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 \fB\-\-trimmomatic\fR used)
.SS "Other options:"
.TP
\fB\-i\fR INT, \fB\-\-max_insert\fR INT
Maximum insert size (includes read length). Reads with
inferred insert size more than the maximum will not be
used to extend contigs [800]
.TP
\fB\-t\fR INT, \fB\-\-threads\fR INT
Number of threads to use [1]
.TP
\fB\-\-kmc_onethread\fR
Force kmc to use one thread. By default the value of
\fB\-t\fR/\-\-threads is used when running kmc
.TP
\fB\-\-strand_bias\fR 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]
.TP
\fB\-\-test\fR
Run using built in test data. All other options will
be ignored, except the mandatory output directory, and
\fB\-\-trimmomatic\fR and \fB\-\-threads\fR can be also be used
.TP
\fB\-\-version\fR
show program's version number and exit