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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. The latest beta version (0.071220.b) supports ABI_3730 as well as older ABI models (373, 377, and 3700), Molecular Dynamics MegaBACE and LI-COR 4000.
- To run it you need to set up PHRED_PARAMETER_FILE variable.
- 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.
- 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. (not tested)
- there has been a number of other papers describing algorithms supposedly superior to phred but working software is not easily obtainable if at all.
See and read!: http://www.cbcb.umd.edu/software/
Genome assemblers used in current genomic projects
- JAZZ -> @JGI in house only
- RAMEN (not published yet as for 10-02-12), used for medaka and silkworm genome sequencing projects
- 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
- Newbler Assembler software from 454 for de novo sequence assembly.
- SHARCGS, a DNA assembly program designed for de novo assembly of 25-40mer input fragments and deep sequence coverage.
- ALLPATHS (HTML) algorithm only
- Maq mapping short reads to an existing genomic sequence
- SOAP suite of programs, no de novo assembly (yet).
- Bowtie "fast and memory efficient"
The most complete list to date is @seqanswers
See also software from
- GSC Software Centre at Canada's Michael Smith Genome Sciences Centre.
Sequence databases & formats
- SRF a generic format for DNA sequence data
- The Short Read Archive @NCBI
Short reads assembly (Solexa etc)
- Velvet Paper(HTML) De Bruijn Graphs based asembler from EBI (Zerbin & Birney)
- Hawkeye interactive visual analytics tool for genome assemblies
- TileQC R based program for quality control of Solexa reads