Top 10 Best Genome Analysis Software & Tools

Genome plays a vital role for various biochemical and physiological activities. Most of the diseases and irregularities caused are due to the underlying factors in genome/genes. Genomic studies enables researchers to identify the genetic flaws in the system of organisms.

Bioinformatics studies have led to the development of best genome analysis software. These powerful tools can be used for breakthrough developments in the genomics, transcriptomics, and Metatranscriptomics studies.

Many high quality tools are open source genome analysis software that are highly cited in published research papers by reputed journals.

What are The Best Genome Analysis Software and Tools?

The best genome analysis software and tools are easily available for use and are often free genome analysis software. They are not just available as public web browsers but have good quality output results (publication-ready quality).

We have prepared a list of top 10 best Genome analysis tools and software. All of these are freely available on web servers for use by researchers. Go for any tool after understanding your research objective and the purpose of the software.

1. SpliceCenter

SpliceCenter is an effective bioinformatics tool for evaluating the impact of gene splicing variation on specific molecular biology techniques. Developed by the Genomics and Bioinformatics Group.

There are multiple tools (visualization and batch) available within the composite package of SpliceCenter. A freely available and user-friendly tool for analysing a sample query genomic sequences of varied organisms.

There are 3 sets of tools for Integrative graphical visualization and three sets of batch tools for evaluating high throughput data from genomic sequences. Performs the task of RNA regions identification and display.


  • Visualization tools include- siRNA-Check, Primer-Check, Peptide-Check
  • Batch tools include- Batch siRNA-Check, Batch-Primer-Check, Batch Peptide-Check
  • Graphical display of siRNA/shRNA target locations within known splice gene variants
  • Evaluation of large number of siRNA/shRNAs via high throughput process
  • Identification of primers/probes

2. Phred

Phred is a base calling program for genomic sequences of DNA. The software is compatible with Windows, MacOS, Linux, UNIX and more. It is available for download from CodonCode Corporation as a part of PHRED-PHRAP package.

The tool is widely used by academic persons and in commercial laboratories during DNA sequencing. It offers easy integration into automated data processing pipelines. The tool does not has GUI. For windows or MacOS users, the user-friendly GUI is available.

Phred reads the DNA sequence chromatogram files and analyses the peaks to call bases and releases quality scores to each base call. CodonCode Aligner is available too.


  • It has high accuracy (40-50% fewer errors are made)
  • Base quality scores produced are highly accurate that is widely accepted
  • The error probabilities are very accurate
  • An ideal tool for quality assessment of genomic sequences


DIALIGN software developed by University of Gottingen is a multiple alignment program at GOBICS. Various versions of the tool are available online on GOBICS web servers. A user-friendly tool for performing the analysis based on genome sequences.

The different versions available are- Anchored DIALIGN, CHAOS DIALIGN, DIALIGN TX, and DIALIGN PFAM. They execute different functions and give different outputs. Users can adjust the parameters before execution of a task.

Jobs such as multiple sequence alignments can be performed and visualization of the results on interactive platforms is feasible.


  • Multiple sequence alignment with optional user-defined constraints
  • CHAOS DIALIGN performs pairwise and multiple alignment of genomic sequences
  • Visualization tool called ABC for viewing alignments
  • Greedy and progressive approaches for segment-based multiple sequence alignment
  • PFAM hits integration in the alignment procedure

4. BioGPS

BioGPS is a free extensible and customisable portal for gene annotation and a reliable source for learning about genome, gene, and protein functions. The software can be used in four ways.

The users can simply search for the gene of interest. The gene annotation report can be viewed interestingly on the platform. The gene report layout can be browsed or searched thoroughly. The users can also build their own Gene and genome reports.

It provides customisable Gene report layout where the user can arrange and control the data display and the way they are displayed. The plug-in library is extensive and can be used according to the needs.


  • Allows to add plug-ins by simple plug-in interface
  • Built on Django web framework with PostgreSQL as the database backend
  • Up to date gene annotation data available
  • Common data sources- NCBI and Ensembl integrated

5. Genome Browser

Genome Browser is a composition of genome analysis tools with various utilities. The tools are publicly available on the free Web servers.

The tools supported by Genome browser are- Batch coordinate conversion tool that converts genome coordinates and annotation files between assemblies. Supports both forward and reverse conversions.

DNA duster tool that removes formatting characters and other non-sequence related characters from an input sequence. Protein duster tool removes formatting characters and other unwanted characters from input sequence


  • Phylogenetic tree PNG maker tool creates PNG image from phylogenetic tree specifications
  • Parameters such as branch length, normalise length, branch labels, legend can be configured
  • Executable and source code downloads of genome browser are available
  • It also supports outside tools such as bedtools, crossmap, makehub, trackhub, wiggletools, BEDOPS, libBigWig


MAGeCK bioinformatics tool also called as model based analysis of genome wide CRISPR-Cas9 knockout is a computational software for identification of relevant genes from the genome scale CRISPR-Cas9 knockout screens technology.

Developed by the Harvard school of Public health/Dana-Farber Cancer Institute is a widely used computational tool. One of the most popular algorithm employed in screening analysis with over 400 citations in reputed research papers.

The tool is very simple to use and has easy pipeline to screen the genes in knockout experiments. It provides documentation and tutorials for the beginners.


  • A highly sensitive tool with low false discovery rate
  • Maintains the source code with new features and fixes the bug
  • Support from the developers and the users community for constant modification
  • Visualisation features enable generation of publication quality figures

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7. Breaking-Cas

Breaking-Cas is a genome based bioinformatics database software constituting the collection of genomes- fungi, plants, invertebrate Metazoa, protists and more. A freely available software that is widely used and cited in recognised journals.

Several parameters for search are provided by the tools such as organism name, several query sequences of DNA in fastA format only upto 20,000 nucleotides. A significant choice for nuclease enzyme is provided that lets you choose the most suitable enzyme.

It is recommended to use the predefined settings for optimised results. Suitable examples and tutorials are also provided to guide the beginners.


  • Used widely for interactive design of a guide RNAs for CRISPR-Cas experiments for ENSEMBL genomes
  • Publication ready results are obtained
  • Flexibility in adjusting the parameters before executing the task
  • Very easy and simple pipeline to use


CRISPOR platform is a program for computational analysis of genomics that helps in designing, evaluating, and a cloning guide sequences for CRISPR/CAS9 system. A publicly available web server tool for free usage.

It can also be downloaded on local machines, compatible with Windows, Linux, OSX platforms. But first, you need to download a virtualBox virtual machine image for Windows/OSX/Linux that includes CRISPOR. For more details on download visit this site.

The tasks are performed in easy three steps. The first step is to enter a single genomic sequence which is less than 2000 base pair, an exon preferably. The second step is for selecting a genome. Out of 637 genomes, you can choose only one for the task. The last step is for selecting a Protospacer Adjacent Motif (PAM).


  • The results are reliable and high-quality
  • Generates results faster with high accuracy
  • Not very high sensitivity hence, low error rates
  • Chromosome range can be given as input instead of sequence
  • Flexibility in choosing a genome and PAM in step two and three respectively


Allele Specific Copy number Analysis of Tumours ASCAT tool is utilised for deriving copy number profiles of tumour cells. The tool in force tumour purity and ploidy from SNP array or massive parallel sequencing data.

ASCAT calculates whole genome Allele specific copy number profiles that is the number of copies of both parental alleles for all the SNP loci across the genome. The tool is also available as a package in R programming.

It is a species independent and works for Illumina and Affymetrix SNP arrays and parallel sequencing data. To increase the sensitivity in samples, ASPCF segmentation algorithm is applied that also lowers noise and increases robustness in noisy samples.


  • The input requires matrices of BAF data
  • The normalisation with specific parameter is available
  • Various analysis can be executed such as GC correction
  • Updated core algorithm for better output and performance
  • Adaptations to allow manual refitting of samples and additions to output data structures

10. CoMet

CoMet is a web server and freely available tool for comparative analysis of Metagenomes based on protein domain signatures.

The server allows to analyse the taxonomic and functional composition of the sample and its comparison with the publicly available data from earlier studies. It follows a very simple and straightforward pipeline to perform all the necessary analysis.

First the DNA sequences are uploaded and then a comprehensive metagenomic analysis including gene prediction, protein domain detection, and metabolic profiling and taxon abundance estimation across all domains of life is performed.


  • More than thousand profiles are pre-computed and stored in the database
  • Faster identification, retrieval and comparison.
  • Provides easily interpretable outputs in graphical formats
  • Tabular data that can be stored off-line for analysis is available
  • In depth statistical comparisons of protein domain counts
  • Gene set enrichment analysis using Gene Ontology terms

In this article, we have elaborately described the best genome analysis software and tools for analysis of genomes of varying known and unknown species. All the tools mentioned here are freely available on the web browsers for use by public.

Many tools are easy to use and have graphic user interface (GUI) for user-friendliness. Command line tools can be a little difficult to handle, for that you can depend on the tutorials and guides provided on the site.

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