export scaffold files from SAM/BAM alignment

[dnajuice]

Using BWA, I have aligned ~10M MiSeq paired end reads to ~100 sequence contigs obtained from non-paired end 454 data. Most of the contigs remained intact after aligning the paired end data, but some were split due to zero coverage.

Is it possible to export the FASTA sequences of the re-shuffled contigs directly from the BAM/SAM files? Furthermore, is there a way to also create the scaffold sequences from the BAM/SAM alignment based on mate pair information?

Would you please let me know if there is a tool/pipeline or an alternative that can do the job?

Thanks very much!