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


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

Durbin R, Dear S. Base qualities help sequencing software. Genome Res 1998

Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer
traces using phred. I. Accuracy assessment. Genome Res 1998 

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

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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