2009/12/1 Edith Schlagenhauf <[email protected]>: > Hi, > > I've got a bunch of output files from a 454/Newbler de novo assembly > for a 8 Mb bacterial genome, ie. various SFF/FASTA/ACE files. > > What are the most appropriate tools/software for viewing/evaluating the > results and for finishing rapidly by automation (there are still several > hundreds of gaps...)? > There is also a cosmid end library available, and various related genomes.
For manual contig inspection and editing, the 'classic' choice is still consed. I'm not sure but I think that it's about 130 years old... What you could try is mapping all your 454 reads against the related genomes to get a second set of contigs. You can then combine your de-novo and your 'mapping' contigs with a program like minimus2. The cosmid library can be added by a scaffolder like bambus. If you've got money to spend, you could do some low coverage large insert size Illlumina sequencing and try to 'scaffold' the contigs using that data. Else you could try different assembly packages (i.e. Mira, Velvet, CA-BOG, Phrap, etc.), and again try to combine your contig sets with minimus2. Also... (I've just come back from an assembly workshop ;-) You could try walking in the Newbler parameter space and seeing if you can 'improve' the assembly (depending on how you want to judge that). For assessing quality of the assembly, try viewing in Hawkeye, and also running the AMOS validate pipeline. Unfortunately, I don't know of any 'automatic finishing' software... Consed will design primers for you though. Do you really need to finish? Try annotating what you have. Currently SeqAnswers seems the place to ask NGS related questions. But don't forget to put bbb in your sig ;-) Dan. > TIA for your input, > Edith > > > > ****************************************** > Dr Edith Schlagenhauf > Bioinformatics > Institute of Plant Biology > University of Zurich > SWITZERLAND > > e-mail: ediths AT botinst DOT uzh DOT ch > ****************************************** > > > > _______________________________________________ > BBB mailing list > [email protected] > http://www.bioinformatics.org/mailman/listinfo/bbb > _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
