Our group has developed a number of software tools that simplify the analysis of next generation sequencing data, largely focused on visualisation.
BLAST Ring Image Generator. BRIG is a cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data.
BRIG can generate figures like this in a matter of minutes:
From Totsika et al. (2011) ‘Insights into a Multidrug Resistant Escherichia coli Pathogen of the Globally Disseminated ST131 Lineage: Genome Analysis and Virulence Mechanisms.’, PLoS ONE 6(10): e26578.
Please cite the BRIG paper if BRIG is used to generate figures for publications:
NF Alikhan, NK Petty, NL Ben Zakour, SA Beatson (2011) BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons, BMC Genomics, 12:402. PMID: 21824423
Easyfig is a Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface (GUI).
EasyFig can generate figures like this in minutes:
If Easyfig is used to generate figures for publication, please cite our paper:
Sullivan MJ, Petty NK, Beatson SA. (2011) Easyfig: a genome comparison visualiser. Bioinformatics; 27 (7): 1009-1010. PMID: 21278367
Contiguity is an interactive software for the visualization and manipulation of de novo genome assemblies. Contiguity creates and displays information on contig adjacency which is contextualized by the simultaneous display of a comparison between assembled contigs and reference sequence.
Read more here.
If you use Contiguity please cite:
Mitchell J Sullivan, Nouri L Ben Zakour, Brian M Forde, Mitchell Stanton-Cook, Scott A Beatson. (2015). Contiguity: Contig adjacency graph construction and visualisation. PeerJ PrePrints 3:e1273 https://doi.org/10.7287/peerj.preprints.1037v1
SeqFindR is a tool to easily create informative genomic feature plots. The publication is in preparation.
From Petty NK and Ben Zakour NL et al. (2014). Global dissemination of a multidrug resistant Escherichia coli clone. Proc Natl Acad Sci U S A. 2014 Apr 15;111(15):5694-9. doi: 10.1073/pnas.1322678111
If you use SeqFindr to generate figures for publication please cite as below:
Stanton-Cook M, Alikhan NF, Forde BM, Ben Zakour NL and Beatson SA (2014) SeqFindR – easily create informative genomic feature plots, http://github.com/mscook/SeqFindR
binCrisp is a Python program that generates figures that shows the distribution of unique spaces sequences from CRISPRs. The program is still under development and is freely available on GitHub.