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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

Data preprocessing

Data processing

Data analysis

Annotation

Data visualization

De novo sequencing analysis workflow

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De novo sequencing analysis workflow schema

Experts in De novo sequencing analysis

They share and annotate bioinformatics tools

Most recent bioinformatics tools

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Nanocorr
Desktop

Nanocorr

An open-source hybrid error correction algorithm. Nanocorr was specifically…

An open-source hybrid error correction algorithm. Nanocorr was specifically developed for Oxford Nanopore reads, because existing packages were incapable of assembling the long read lengths (5-50…

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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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S-MART
Desktop

S-MART

Performs tasks required for the analysis of mapped RNA-Seq reads. S-MART…

Performs tasks required for the analysis of mapped RNA-Seq reads. S-MART performs different categories of tasks: (i) it can filter and select the data of most interest, cluster the information to…

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SEECER
Desktop

SEECER SEquencing Error CorrEction for Rna reads

Performs error correction in RNA-Seq data. SEECER is a method based on profile…

Performs error correction in RNA-Seq data. SEECER is a method based on profile a hidden Markov Model (HMMs). This method does not require a reference genome. It can handle non-uniform coverage and…

Most popular analytical software and databases

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SAMtools
Desktop

SAMtools

A suite of programs for interacting with high-throughput sequencing data. It…

A suite of programs for interacting with high-throughput sequencing data. It can manipulate alignments in the SAM/BAM/CRAM formats : reading, writing, editing, indexing, viewing and converting…

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Bowtie
Desktop

Bowtie

A short read aligner that aligns short DNA sequences (reads) to the human…

A short read aligner that aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its…

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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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Trimmomatic
Desktop

Trimmomatic

Performs a variety of trimming tasks for Illumina paired-end and single ended…

Performs a variety of trimming tasks for Illumina paired-end and single ended data. Trimmomatic is a flexible, pair-aware preprocessing tool, optimized for Illumina next-generation sequencing (NGS)…

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