hi everybody I'm working whit 454 single end sequences obtained from two different species. I need to compare the two thesis. Until now i used Abyss tools, for each one, in the following order: ABYSS with different kmer, abyss-fac to chose the best assembly, Adjlist, popbubbles and mergecontigs. Now which are the best programmes to use to compare the two assembly? Kalign may be? And which commands have i to use? An other question: when i use ABYSS to assembly the sequence i need to use the command se-contig? thank you very much!
Check the new Abyss manual:
You may also think about improving the assemblies by performing error correction before the assembly. It did work for me for Illumina reads, but it also has an option for 454:
As for the assembly comparisons, it depends on quality of your draft assemblies and the level of coverage. If you have any related species with a more accurate genome assembly this will help.