Table 1

Comparison of some of the currently avaibale tools for data interpretaion and analysis
Tool Operating system Language Database Alignment format Data file formats
ABC[14] Win, Linux, and OS X JAVA Multiple sequence alignments and data typically associated with alignments NA NA
EagleView[15] Win, Linux, Mac OS X NA Next-generation sequencing data NA ACE format (commonly used by genome assembly programs), READS, EGI, MAP
LookSeq[16] An AJAX based web viewer. Requires a standard web browser Perl, AJAX Illumina genome analyzer sequencing data 1. Both CIGAR and new sequencing technology alignment data NA
2. SAM/BAM format of SAM tools
Magic Viewer[17] Win Java Next-generation sequencing data NA SAM format- enables an easy conversion of various input file formats, including PSL, MAQ, Bowtie, SOAP, ZOOM
Tablet[18] Windows, OS X, Linux, Solaris Java ACE, AFG, MAQ and SOAP assembly formats. Also 454 and Solexa data NA NA
GenomeGems Win MATLAB Next-generation sequencing data, analyzed by MAQ, Variant SNP Classifier, and SNVMix in, a pre-determined ‘.txt’ format Especially MAQ, but also Variant SNP Classifier and SNVMix Reads '.txt’ file format with columns separated by tab

Abbreviations: NA, not available; MAQ, Mapping and Assembly with Quality; SOAP, Short Oligonucleotide Analysis Package; ACE, Archive Compression Extension; AFG, Auxiliary File Generator; EGI, Embedded Gateway Interface; SNVMix, Small Nucleotide Variants; CIGAR, Compact Idiosyncratic Gapped Alignment Report.

Ben-Zvi et al.

Ben-Zvi et al. BMC Research Notes 2012 5:338   doi:10.1186/1756-0500-5-338

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