Interlude: Converting PacBio's BAM to FASTA
PacBio reads are now output from their sequencing instruments in BAM format (http://pacbiofileformats.readthedocs.org/en/3.0/BAM.html). As our tools only work with FASTA or FASTQ, we recommend that you convert the reads to FASTA format using samtools (https://github.com/samtools/samtools). Once you have samtools up and running, the following command does the trick:
samtools fasta -0 raw_reads.fa original_pacbio_reads.bam