Wikiomics:DNA sequencing
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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.
- To run it you need to set up PHRED_PARAMETER_FILE variable.
Bash shell:
export PHRED_PARAMETER_FILE=/path/to/your/file/phredpar.dat
- To see all the options:
phred -doc | less
- 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
- 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
