Wikiomics:DNA sequencing: Difference between revisions
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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. | ||
* [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.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. | * [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. | ||
Revision as of 15:25, 24 June 2008
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.
- 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
- 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).
- Newbler Assembler software from 454 for de novo sequence assembly.
See also software from
- GSC Software Centre at Canada's Michael Smith Genome Sciences Centre.
Short reads assembly (Solexa etc)
- Velvet Paper(HTML) De Bruijn Graphs based asembler from EBI (Zerbin & Birney)
Contig ordering/finishing
- Hawkeye interactive visual analytics tool for genome assemblies
