Assembly Packages for Large Scale Genome Sequencing, Genomic, DNA Sequence, FASTA, PHRED

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Assembly packages for large-scale genome sequencing

Assembly packages are used for assembling small shotgun sequences generated by automatic sequencers into contiguous sequences called contigs. Such packages have become important for assembly of genomic as well as cDNA sequences

PHRED (base calling software with quality identification).

It reads data generated from automatic DNA sequencers (sequencer models, ABI373, ABI377 and ABI3700), calls bases, assigns quality values to the bases and writes the base call and quality values to output files in FASTA format or PHRED files (also called PHD files). The output files can be used by PHRAP sequences assembly programme, described in the next para. (base calling means assigning bases to peaks of different colours obtained as output from automatic sequencers; quality values are assigned on the basis of heights of the peaks)

PHRAP (fragment assembly programme or Phill’s revised assembly programme)

It is a programme for assembling shotgun DNA sequence data. It constructs contig sequences, each as a mosaic of high quality parts of read-out, removing the consensus sequences, having low quality values

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