Table 1 Comparison of some of the currently avaibale tools for data interpretaion and analysis
From: GenomeGems: evaluation of genetic variability from deep sequencing data
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 |