De novo genome sequencing data analysis bioinformatics software tools

De novo genome sequencing involves sequencing a novel genome for the first time, and requires specialized assembly of sequencing reads. The low cost and increasing availability of NGS data have driven a growing interest in software tools for de novo genome sequencing analysis.…

De novo sequencing analysis steps

De novo sequencing analysis workflow

Click the icons of the schema to view tools

De novo sequencing analysis workflow schema

Most recent bioinformatics tools

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EULER-GA
Web

EULER-GA Euler Genome Assembler

Manages reads in highly repetitive regions. EULER-GA uses repeats as a fragment…

Manages reads in highly repetitive regions. EULER-GA uses repeats as a fragment assembly tool for DNA sequences.

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SIMBA
Desktop

SIMBA SImple Manager for Bacterial Assemblies

Manages assembly projects of bacterial genomes with Next Generation Sequencing…

Manages assembly projects of bacterial genomes with Next Generation Sequencing (NGS) platforms. SIMBA is composed of three parts: (i) projects is a module which permits to administer sequencing…

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EULER-AIR
Desktop

EULER-AIR

Detects and corrects base assignment errors in genome assembly projects.…

Detects and corrects base assignment errors in genome assembly projects. EULER-AIR is based on an Expectation-Maximization (EM) algorithm and can help to design efficient finishing experiments…

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deBGR
Desktop

deBGR

Supplies an approximate representation of the weighted de Bruijn Graph. deBGR…

Supplies an approximate representation of the weighted de Bruijn Graph. deBGR was built on the prototype k-mer counter Squeakr.

Most popular analytical software

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SV-STAT
Desktop

SV-STAT Structural Variation detection by STAck and Tail

Quantifies evidence for structural variation in genomic regions suspected of…

Quantifies evidence for structural variation in genomic regions suspected of harboring rearrangements. SV-STAT extends existing methods by adjusting a chimeric read’s support of a structural…

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Ray
Desktop

Ray

Assembles reads obtained with new sequencing technologies (Illumina, 454,…

Assembles reads obtained with new sequencing technologies (Illumina, 454, SOLiD) using MPI 2.2. Ray allows to reduce the number of contigs and the number of errors. It can serve as a basis to develop…

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SSAKE
Desktop

SSAKE

Provides a de novo assembler for short DNA sequence reads. SSAKE is designed to…

Provides a de novo assembler for short DNA sequence reads. SSAKE is designed to help leverage the information from short sequences reads by assembling them into contigs and scaffolds that can be used…

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SPAdes
Desktop

SPAdes

A single-cell assembler for capturing and sequencing “microbial dark…

A single-cell assembler for capturing and sequencing “microbial dark matter” that forms small pools of randomly selected single cells (called a mini-metagenome) and further sequences all genomes…

Curators for De novo sequencing analysis

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