Paketti: iva (1.0.11+ds-5)

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Kotisivu [github.com]

Samankaltaisia paketteja:

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.

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

Muut pakettiin iva liittyvät paketit

depends

recommends

suggests

enhances

dep: default-jre-headless

Standard Java or Java compatible Runtime (headless)
dep: fastaq

FASTA and FASTQ file manipulation tools
dep: kmc

count kmers in genomic sequences
dep: mummer

Efficient sequence alignment of full genomes
dep: perl

Larry Wallin kieli tekstitiedostojen analysointia ja raportointia varten
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 language (Python 3)
dep: python3-packaging

core utilities for python3 packages
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

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