Wikiomics:DNA sequencing

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.

Sequence assembly

See and read!: http://www.cbcb.umd.edu/software/

First generation

• phrap
• TIGR assembler
• CAP3 WWW@Pasteur

Genome assemblers used in current genomic projects

• Arachne @Broad Inst (largest number of citations)
• Phusion @Sanger
• Atlas @Baylor

• JAZZ -> @JGI in house only
• RAMEN (not published yet??, used for medaka and silkworm 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).

• 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)

Contig ordering/finishing

• Hawkeye interactive visual analytics tool for genome assemblies