The data I have is sequencing of fragmented whole genomic DNA from several individuals of S. purpuratus (purple sea urchin), all as .FASTQ file format. I have an index of the genome to align and produce .bam output files. I have tried to identify indels, but only got a few small SNPs. I am looking for much larger insertions or deletions. I think that tophat might be detecting differences between the fastq file and the genome index only. I want to be able to detect indels across multiple fastq files. The differences (large size insertions and deletions) I want to detect are between the FASTQ files, not in the FASTQ versus the reference genome. Does anyone know of a good workflow to identify indels by simply aligning multiple fastq files?