PHRAP & CONSED

Dr. Andrew G. McArthur mcarthur at evol5.mbl.edu
Wed Mar 24 22:21:10 EST 1999


Colleagues,

I wish to create a bibliography of papers relating to the use of PHRAP and
CONSED for shotgun genomic sequencing.  Please email me the citation of
any relevant papers and I will forward the entire bibliography to the list
once complete.  Below is a seed for the bibliography.

Much thanks,

Dr. Andrew G. McArthur
Giardia Genome Project
www.mbl.edu/Giardia

---------
Durbin R, Dear S. Base qualities help sequencing software. Genome Res 1998
Mar;8(3):161-2.

Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer
traces using phred. I. Accuracy assessment. Genome Res 1998 
Mar;8(3):175-85.

Ewing B, Green P. Base-calling of automated sequencer traces using phred.
II. Error probabilities. Genome Res 1998 Mar;8(3):186-94 .

Gordon D, Abajian C, Green P. Consed: a graphical tool for sequence
finishing. Genome Res 1998 Mar;8(3):195-202.

Nickerson DA, Tobe VO, Taylor SL. PolyPhred: automating the detection and
genotyping of single nucleotide substitutions using fluorescence-based
resequencing. Nucleic Acids Res 1997 Jul 15;25(14):2745-51.

Richterich P. Estimation of errors in "raw" DNA sequences: a validation
study. Genome Res 1998 Mar;8(3):251-9.

Rieder MJ, Taylor SL, Tobe VO, Nickerson DA. Automating the identification
of DNA variations using quality-based fluorescence re-sequencing: analysis
of the human mitochondrial genome. Nucleic Acids Res 1998 Feb
15;26(4):967-73.

Smith TM, Abajian C, Hood L. Hopper: software for automating data tracking
and flow in DNA sequencing. Comput Appl Biosci 1997 Apr;13(2):175-82.

Wendl MC, Dear S, Hodgson D, Hillier L. Automated sequence preprocessing
in a large-scale sequencing environment. Genome Res 1998 Sep;8(9):975-84.







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