iva

iterative virus sequence assembler

Command lineScience

Not tested on a device yet. What that means

Commands in the package

iva
iva_qc
iva_qc_make_db

About iva

From Debian's package description

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 depth.
IVA's main algorithm works by iteratively extending contigs using aligned read pairs. Its input can be just read pairs, or additionally you can provide an existing set of contigs to be extended. Alternatively, it can take reads together with a reference sequence.

From Debian's description of the iva package, under that package's license.

Dependencies

Depends on

fastaq
python3-networkx
python3-packaging
python3-pysam
python3
perl
kmc
mummer
smalt
samtools
python3-numpy
default-jre-headless

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Sources and licenses

Name: the Debian package name.
Summary: Debian's short description of the iva package, under that package's license.
Description: Debian's description of the iva package, under that package's license.
Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
Popularity: Debian Popularity Contest counts.