|sw summary=Nesoni is a high-throughput sequencing data analysis toolset.|bio domain=RNA-Seq alignment, SNP detection, Phylogenetics,|bio method=Sequence alignment,|bio tech=Illumina, 454, ABI SOLiD,|created at=Victorian Bioinformatics Consortium|maintained=Yes|input format=SAM, FASTA,|sw feature=largely for bacterial genomes|language=Python,}}Nesoni is a high-throughput sequencing data analysis tool set, which the VBC has developed to cope with the flood of Illumina, 454, and SOLiD data now being produced.

Our work is largely with bacterial genomes, and the design tradeoffs trade-offs in nesoni reflect this.

Nesoni focusses on analysing the alignment of reads to a reference genome. We use the [[SHRiMP ]] read aligner, as it is able to detect small insertions and deletions in addition to SNPs.

Nesoni can call a consensus of read alignments, taking care to indicate ambiguity. This can then be used in various ways: to determine the protein level changes resulting from SNPs and indels, to find differences between multiple strains, or to produce n-way comparison data suitable for phylogenetic analysis in [[SplitsTree4]].

|bio domain=RNA-Seq, {{Links}}|created at=Victorian Bioinformatics Consortium|input format=SAM, FASTA,{{References}}{{Link box}}