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.
- 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.
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??, used for medaka and silkworm projects)
- 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 (http://www.genome.org/cgi/content/abstract/gr.074492.107v1 +Paper) De Bruijn Graphs based asembler from EBI (Zerbin & Birney)
- Hawkeye interactive visual analytics tool for genome assemblies