Links for assembly softwares
Ace.mbly
  • ftp.crbm.cnrs-mop.fr/pub/unix/acembly/
    • AutoAssembler
  • perkin-elmer.com/ga/237506/237506.html
  • Parker, S. R. 1997. AutoAssembler sequence assembly software. Methods Mol Biol. 70:107-17.
    • BaseFinder
  • smithlab.chem.wisc.edu/Research/informatics.html
  • Giddings, M. C., J. Severin, M. Westphall, J. Wu, and L. M. Smith. 1998. A software system for data analysis in automated DNA sequencing. Genome Res. 8:644-65.
    • CAP2
  • cs.mtu.edu/faculty/Huang.html
  • Huang, X. 1996. An improved sequence assembly program. Genomics. 33:21-31.
    • Consed
  • bozeman.mbt.washington.edu/
  • Gordon, D., C. Abajian, and P. Green. 1998. Consed: a graphical tool for sequence finishing. Genome Res. 8:195-202.
    • Cross_match
  • bozeman.mbt.washington.edu/
    • Factura
  • perkin-elmer.com/ga/237506/237506.html
  • Parker, S. R. 1997. AutoAssembler sequence assembly software. Methods Mol Biol. 70:107-17.
    • Faktory
  • cs.arizona.edu/faktory/
    • GASP
  • genome.wustl.edu/gsc/Informatics/software.shtml
  • Wendl, M. C., S. Dear, D. Hodgson, and L. Hillier. 1998. Automated sequence preprocessing in a large-scale sequencing environment. Genome Res. 8:975-84.
    • GeneJockeyII
  • biosoft.com/genejock.htm
  • Taylor, P. 1997. GeneJockeyII. DNA sequencing and fragment assembly. Methods Mol Biol. 70:91-106.
    • GFP
  • stork.cellb.bcm.tmc.edu/gfp
    • GRM
  • kiwi.bcm.tmc.edu:8088/GRM
  • Lawrence, C. B., S. Honda, N. W. Parrott, T. C. Flood, L. Gu, L. Zhang, M. Jain, S. Larson, and E. W. Myers. 1994. The genome reconstruction manager: a software environment for supporting high-throughput DNA sequencing. Genomics. 23:192-201.
    • Lucy
  • tigr.org/softlab/
    • MTT
  • hgc.lbl.gov/inf/mtt.html
  • E. Veklerov, F. Eeckman, C. Martin. 1996. MTT: a software tool for quality control in sequence assembly. Microbial Comparative Genomics, v. 1, No. 3.
    • Phrap
  • bozeman.mbt.washington.edu/
    • Phred
  • bozeman.mbt.washington.edu/
  • Ewing, B., L. Hillier, M. C. Wendl, and P. Green. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Research. 8:175-85.
  • Ewing, B., and P. Green. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Research. 8:186-94.
  • Giddings, M. C., J. Severin, M. Westphall, J. Wu, and L. M. Smith. 1998. A software system for data analysis in automated DNA sequencing. Genome Res. 8:644-65.
  • Richterich, P. 1998. Estimation of errors in "raw" DNA sequences: a validation study. Genome Res. 8:251-9.
    • Pride
  • dkfz-heidelberg.de/tbi/services/Pride/prideform
  • Haas, S., M. Vingron, A. Poustka, and S. Wiemann. 1998. Primer design for large scale sequencing. Nucleic Acids Res. 26:3006-12.
    • Primo
  • gestec.swmed.edu/gestec2.htm
  • Li, P., K. C. Kupfer, C. J. Davies, D. Burbee, G. A. Evans, and H. R. Garner. 1997. PRIMO: A primer design program that applies base quality statistics for automated large-scale DNA sequencing. Genomics. 40:476-85.
    • SeqManII
  • dnastar.com/products/products.html
  • Swindell, S. R., and T. N. Plasterer. 1997. SEQMAN. Contig assembly. Methods Mol Biol. 70:75-89.
    • SPASS/SPACE
  • hgc.lbl.gov/inf/spass.html
    • Staden Package (GAP4 softwares)
  • mrc-lmb.cam.ac.uk/pubseq/
  • Staden, R. 1996. The Staden sequence analysis package. Mol Biotechnol. 5:233-41.
  • Bonfield, J. K., K. Smith, and R. Staden. 1995. A new DNA sequence assembly program. Nucleic Acids Res. 23:4992-9.
  • Bonfield, J. K., and R. Staden. 1995. The application of numerical estimates of base calling accuracy to DNA sequencing projects. Nucleic Acids Res. 23:1406-10.
  • Bonfield, J. K., and R. Staden. 1996. Experiment files and their application during large-scale sequencing projects. DNA Seq. 6:109-17.
    • TIGR Assembler
  • tigr.org/softlab/
  • Sutton, G., O. White, M. Adams, and A. Kerlavage. 1995. TIGR Assembler: A new tool for assembling large shotgun sequencing projects. Genome Science and Technology. 1:9-19.
    • For random shotgun strategy, see also :
    CAFTOOLS
  • sanger.ac.uk/Software/formats/CAF/
  • Dear, S., R. Durbin, L. Hillier, G. Marth, J. Thierry-Mieg, and R. Mott. 1998. Sequence assembly with CAFTOOLS. Genome Res. 8:260-7.
    • For ordered shotgun strategy (OSS), see also :
    CloneSpacer
  • Singh, G. B., and S. A. Krawetz. 1995. CLONEPLACER: a software tool for simulating contig formation for ordered shotgun sequencing. Genomics. 25:555-8.
    • For finger printing shotgun strategy, see also :
    MCD (and ATLAS)
  • Gillett, W., L. Hanks, G. K. S. Wong, J. Yu, R. Lim, and M. V. Olson. 1996. Assembly of high-resolution restriction maps based on multiple complete digests of a redundant set of overlapping clones. Genomics. 33:389-408.
    • FPC
  • sanger.ac.uk/Users/cari/fpc.shtml
  • Soderlund, C., I. Longden, and R. Mott. 1997. FPC: a system for building contigs from restriction fingerprinted clones. Comput Appl Biosci. 13:523-35.

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