Interlude: Converting PacBio's BAM to FASTA

PacBio reads are now output from their sequencing instruments in BAM format ( As our tools only work with FASTA or FASTQ, we recommend that you convert the reads to FASTA format using samtools ( Once you have samtools up and running, the following command does the trick:

samtools fasta -0 raw_reads.fa original_pacbio_reads.bam