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- Accessing sequence data from local and remote databases
- Transforming formats of database/ file records
- Manipulating individual sequences
- Searching for similar sequences
- Creating and manipulating sequence alignments
- Searching for genes and other structures on genomic DNA
- Developing machine readable sequence annotations
phred, phrap, consed, etc...
The phred software reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base. See the site for descriptions of the other bundled software.
GATK
GATK was designed to simplify the process of developing efficient, robust tools for working with NGS data, and currently supports in a single integrated framework Solexa, SOLiD, 454, Complete Genomics, and Sanger sequencer data.
IGV
The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated datasets.
polyphred
PolyPhred is a program that compares fluorescence-based sequences.