Wikiomics:DNA sequencing

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(basecalling & assembly)
m (Base calling (ABI))
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* [http://www.phrap.com/phred/ phred] giving more accurate calls for less accurate part of the sequence (like at the end of the run, say 600bp and more) . Phred also gives a probability/quality values for each of the bases allowing more accurate assembly.  
* [http://www.phrap.com/phred/ phred] giving more accurate calls for less accurate part of the sequence (like at the end of the run, say 600bp and more) . Phred also gives a probability/quality values for each of the bases allowing more accurate assembly.  
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* [http://www.nucleics.com/ Long Trace & Peak Trace] from Nucleics. Claims to increase the lenght of readable bases by ca 80bp. Separate software module for increasing daily throughput of a cspillary sequencer.
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* [http://www.nucleics.com/ Long Trace & Peak Trace] from Nucleics. Claims to increase the lenght of readable bases by ca 80bp. Separate software module for increasing daily throughput of a capillary sequencer.
=Sequence assembly=
=Sequence assembly=

Revision as of 02:37, 12 June 2008

Contents

Base calling (ABI)

  • phred giving more accurate calls for less accurate part of the sequence (like at the end of the run, say 600bp and more) . Phred also gives a probability/quality values for each of the bases allowing more accurate assembly.
  • Long Trace & Peak Trace from Nucleics. Claims to increase the lenght of readable bases by ca 80bp. Separate software module for increasing daily throughput of a capillary sequencer.

Sequence assembly

See and read!: http://www.cbcb.umd.edu/software/

First generation

Genome assemblers used in current genomic projects

  • JAZZ -> @JGI in house only
  • RAMEN (not published yet??, used for medaka and silkworm projects)

New Programs

  • Minimus suitable for bacterial genomes, part of AMOS
  • [AMOS A Modular Open-Source Assembler
  • EULER P.Pevzner graph algorithm producing superior contigs

requires phrap and patched ReAligner

  • MIRA latest version 2.9.25 enables true hybrid sequence assembly (454 data [GS20 or GS FLX], Solexa with Sanger reads).

See also software from

Contig ordering/finishing

  • Hawkeye interactive visual analytics tool for genome assemblies
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