Data visualisation
Data visualization with GATC Viewer, UCSC Genome Browser
We recommend the following bioinformatics tools for illustrative and clear data visualization:
- GATC Viewer for raw data from ABI 3730 xl (Sanger sequencing)
- Hawkeye for analyses of genome assemblies and validations, also helpful for the identification and correction of assembly errors, among other things
- EagleView; an informative visualization tool for genome assemblies and available for Windows, Linux and Mac.
- Windows Excel to view tables to search for positional polymorphisms and structural variations
- UCSC genome browser to visualize GFF files
Scaffolding of sequencing projects with long insert Illumina reads
Spotlight
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Useful Links
Roche GS De Novo Assembler (454 Life Science / Roche)
MIRA (Mimicking Intelligent Read Assembly, Bastien Chevreux)
Velvet (EMBL-EBI, Cambridge, UK)
Edena (Exact De Novo Assembler)
ELAND (Efficient Large-Scale Alignment of Nucleotide Databases)
Mosaik (Reference guided aligner/assembler)
MAQ (Mapping and Assembly with Qualities)
SOAP (Short Oligonucleotide Alignment Program)
More software for Next Generation sequencing...
