IonCRAM: a reference-based compression tool for ion torrent sequence files

摘要

Flow Signals and their position in the SAM/BAM file. The upper part shows an example DNA fragment to be sequenced by an Ion Torrent machine. The key and bar code sequences are ligated (pre-pended) to the fragment. The key sequence (TCAG) is a control sequence to ensure correct sequencing. A barcode sequence is added to a certain group of fragments. The use of barcodes makes it possible to sequence the DNA of different samples/patients in one run. The lower part of the figure shows a schematic representation of the fields in the SAM file. The SAM file is the non-binary readable version of the BAM. The header part includes the flow cycle and the key sequence. Each line in the SAM file represents one read, aligned to the reference genome. The remaining rows include the read information in a tab-separated format: We show only the columns/fields of relevance to this paper. We show the fields including the read ID, the physical position and the CGAR string which represents the alignment, the bases of the DNA sequence in the read, the quality field, and the flow signals in the ZM field