Wikiomics:DNA sequencing

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* [http://www.454.com/enabling-technology/the-software.asp Newbler Assembler] software from 454 for de novo sequence assembly.
* [http://www.454.com/enabling-technology/the-software.asp Newbler Assembler] software from 454 for de novo sequence assembly.
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====Experimental====
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* [http://sharcgs.molgen.mpg.de/index.shtml SHARCGS], a DNA assembly program designed for de novo assembly of 25-40mer input fragments and deep sequence coverage.
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* [http://www.genome.org/cgi/content/full/18/5/810 ALLPATHS (HTML)] algorithm only
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* [http://maq.sourceforge.net/maq-man.shtml Maq] mapping short reads to an existing genomic sequence
See also software from  
See also software from  
* [http://www.bcgsc.ca/platform/bioinfo/software/ GSC Software Centre] at Canada's Michael Smith Genome Sciences Centre.
* [http://www.bcgsc.ca/platform/bioinfo/software/ GSC Software Centre] at Canada's Michael Smith Genome Sciences Centre.
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===Sequence databases & formats===
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* [http://srf.sourceforge.net/ SRF] a generic format for DNA sequence data
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* [http://www.ncbi.nlm.nih.gov/Traces/sra/ The Short Read Archive @NCBI]
===Short reads assembly (Solexa etc)===
===Short reads assembly (Solexa etc)===

Revision as of 14:16, 30 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. Quality scores range from 4 to about 60, the "high quality bases" are these with scores > 20.
  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).
  • SSAKE program for assembly milions of short sequences

Experimental

  • SHARCGS, a DNA assembly program designed for de novo assembly of 25-40mer input fragments and deep sequence coverage.
  • Maq mapping short reads to an existing genomic sequence

See also software from


Sequence databases & formats

Short reads assembly (Solexa etc)

Contig ordering/finishing

  • Hawkeye interactive visual analytics tool for genome assemblies
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