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