Wikiomics:DNA sequencing

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m (Base calling (ABI))
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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 +
#To run it you need to set up PHRED_PARAMETER_FILE variable.
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Bash shell:
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<pre>
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export PHRED_PARAMETER_FILE=/path/to/your/file/phredpar.dat
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</pre>
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 +
#To see all the options:
 +
<pre>
 +
phred -doc | less
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</pre>
 +
 +
#To do simple basecalling on _all_ files in a input_directory and store the SCF files in scf_output_directory:
 +
<pre>
 +
phred -id input_directory -cd scf_output_directory:
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</pre>
 +
 +
Caveat: names of the new SCF files will be the same as input files.
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 +
* [http://www.genome.org/cgi/content/full/11/5/875 LifeTrace] from Incyte. Usage info from [https://www.cebitec.uni-bielefeld.de/cgi-bin/man.cgi?section=1&topic=lifetrace U.Bielefeld]. Comparable with phred, better than phred on MegaBACE sequences. Not available from original Incyte web site (080624).  
* [http://www.genome.org/cgi/content/full/11/5/875 LifeTrace] from Incyte. Usage info from [https://www.cebitec.uni-bielefeld.de/cgi-bin/man.cgi?section=1&topic=lifetrace U.Bielefeld]. Comparable with phred, better than phred on MegaBACE sequences. Not available from original Incyte web site (080624).  

Revision as of 10:12, 8 July 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.
  1. To run it you need to set up PHRED_PARAMETER_FILE variable.

Bash shell:

export PHRED_PARAMETER_FILE=/path/to/your/file/phredpar.dat
  1. To see all the options:
phred -doc | less
  1. To do simple basecalling on _all_ files in a input_directory and store the SCF files in scf_output_directory:
phred -id input_directory -cd scf_output_directory:

Caveat: names of the new SCF files will be the same as input files.


  • LifeTrace from Incyte. Usage info from U.Bielefeld. Comparable with phred, better than phred on MegaBACE sequences. Not available from original Incyte web site (080624).
  • 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 as for 08-6-17), used for medaka and silkworm genome sequencing 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

Short reads assembly (Solexa etc)

Contig ordering/finishing

  • Hawkeye interactive visual analytics tool for genome assemblies
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