Iterative Virus Assembler - de novo virus assembler of Illumina paired reads.
PLEASE NOTE: we currently do not have the resources to provide support for IVA, so please do not expect a reply if you flag any issue.
IVA is a de novo assembler designed to assemble virus genomes that have no repeat sequences, using Illumina read pairs sequenced from mixed populations at extremely high and variable depth.
For more information, please read the IVA publication.
For installation instructions, please refer to the IVA website
The test can be run with dzil from the top level directory:
python setup.py test
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
For usage help and examples, see the IVA wiki page.
IVA is free software, licensed under GPLv3.
Please report any issues to the issues page.
PLEASE NOTE: we currently do not have the resources to provide support for IVA, so please do not expect a reply if you flag any issue.
If you use this software please cite:
IVA: accurate de novo assembly of RNA virus genomes.
Hunt M, Gall A, Ong SH, Brener J, Ferns B, Goulder P, Nastouli E, Keane JA, Kellam P, Otto TD.
Bioinformatics. 2015 Jul 15;31(14):2374-6. doi: 10.1093/bioinformatics/btv120. Epub 2015 Feb 28.
Adapter sequences:
Optimal enzymes for amplifying sequencing libraries.
Quail, M. a et al. Nat. Methods 9, 10-1 (2012).
GAGE:
GAGE: A critical evaluation of genome assemblies and assembly algorithms.
Salzberg, S. L. et al. Genome Res. 22, 557-67 (2012).
KMC:
Disk-based k-mer counting on a PC.
Deorowicz, S., Debudaj-Grabysz, A. & Grabowski, S. BMC Bioinformatics 14, 160 (2013).
Kraken:
Kraken: ultrafast metagenomic sequence classification using exact alignments.
Wood, D. E. & Salzberg, S. L. Genome Biol. 15, R46 (2014).
MUMmer:
Versatile and open software for comparing large genomes.
Kurtz, S. et al. Genome Biol. 5, R12 (2004).
R:
R: A language and environment for statistical computing.
R Core Team (2013). R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org/.
RATT:
RATT: Rapid Annotation Transfer Tool.
Otto, T. D., Dillon, G. P., Degrave, W. S. & Berriman, M. Nucleic Acids Res. 39, e57 (2011).
SAMtools:
The Sequence Alignment/Map format and SAMtools.
Li, H. et al. Bioinformatics 25, 2078-9 (2009).
Trimmomatic:
Trimmomatic: A flexible trimmer for Illumina Sequence Data.
Bolger, A. M., Lohse, M. & Usadel, B. Bioinformatics 1-7 (2014).
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