I have read the documentation for bambus, it needs contig file which contain read mapping informations,
in my current project, the sequence contigs is build from short-read sequences (generated by SOLEXA or SOLID), thus the contig files are very large,
and several pair-end informations is present, thus scaffolding for short-read assembled contigs with bambus is not possible.
i have generated scaffolds from these short-read contigs using pair-end informations with some other tools,
when only scaffold files (fasta) and mapping informations to close genome and BAC -end sequence is available,
is it possible to link these scaffolds into larger pieces using other informations -such as mapping to close genomes / physical maps,
without using contig files
if this can be done, how can i specify the input files?
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