Package: iva (1.0.9+ds-11)

[ Source: iva  ]

iterative virus sequence assembler

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.

Tags: Biology: Nucleic Acids, Field: Biology, field::biology:bioinformatics, implemented-in::python, User Interface: Command Line, Role: role::program, works-with::biological-sequence, Works with: Files

Other Packages Related to iva

• dep: default-jre-headless

  Standard Java or Java compatible Runtime (headless)

• dep: fastaq (>= 1.6)

  FASTA and FASTQ file manipulation tools

• dep: kmc

  count kmers in genomic sequences

• dep: mummer

  Efficient sequence alignment of full genomes

• dep: perl

  Larry Wall's Practical Extraction and Report Language

• dep: python3

  interactive high-level object-oriented language (default python3 version)

• dep: python3-networkx

  tool to create, manipulate and study complex networks (Python3)

• dep: python3-numpy

  Fast array facility to the Python 3 language

• dep: python3-pysam

  interface for the SAM/BAM sequence alignment and mapping format (Python 3)

• dep: samtools

  processing sequence alignments in SAM, BAM and CRAM formats

• dep: smalt

  Sequence Mapping and Alignment Tool

• rec: bioperl

  Perl tools for computational molecular biology

• rec: r-base-core

  GNU R core of statistical computation and graphics system

• rec: trimmomatic

  flexible read trimming tool for Illumina NGS data

Download iva

Download for all available architectures

Architecture	Package Size	Installed Size	Files
amd64	8,377.6 kB	8,765.0 kB	[list of files]
arm64	8,377.6 kB	8,765.0 kB	[list of files]
armel	8,377.6 kB	8,765.0 kB	[list of files]
armhf	8,377.6 kB	8,765.0 kB	[list of files]
i386	8,377.6 kB	8,765.0 kB	[list of files]
mips64el	8,377.6 kB	8,765.0 kB	[list of files]
mipsel	8,377.6 kB	8,765.0 kB	[list of files]
ppc64el	8,377.6 kB	8,765.0 kB	[list of files]