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

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De novo sequencing analysis workflow schema

Most recent bioinformatics tools

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ANAQUIN
Desktop

ANAQUIN

Facilitates the analysis of spike-in controls for next generation sequencing…

Facilitates the analysis of spike-in controls for next generation sequencing (NGS). ANAQUIN offers a way for users to evaluate the performance of spike-in controls and the accompanying RNA/DNA…

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IDBA
Desktop

IDBA Iterative De Bruijn graph de novo Assembler

Alleviates the difficulties in setting a correct k and the filtering threshold…

Alleviates the difficulties in setting a correct k and the filtering threshold m. IDBA can capture good contigs and these contigs can be made longer as k increases. It comports an initial filtering…

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LRCstats
Desktop

LRCstats

Provides a novel way to measure the accuracy of sequencing errors correction…

Provides a novel way to measure the accuracy of sequencing errors correction methods in case where realistic simulators exist. LRCstats has been developed to complement the SimLORD simulator for…

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HECIL
Desktop

HECIL Hybrid Error Correction with Iterative Learning

Allows decomposition of the workload into independent data-parallel tasks that…

Allows decomposition of the workload into independent data-parallel tasks that can be executed simultaneously. HECIL is a hybrid correction framework that computes erroneous long reads based on…

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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