ContextMap 2.0

The standalone ContextMap 2.0 algorithm consists of five major steps (see figure below):

(A) In the first step, ContextMap 2.0 aligns reads to a given reference genome using a modified Bowtie version that performs alignments in forward and backward direction to also detect reads from exon-exon junctions (split reads).

(B) These initial alignments are then used to calculate contexts, defined as reads originating from the same stretch of genome. For this purpose, ContextMap clusters read alignments based on their genomic starting position, allowing multiple alignments of reads. Extension of alignments and identification of the most likely mapping for each read is then performed independently for each context (steps C-D) with integration performed only in the last step (E). This strategy allows ContextMap to make heavy use of multi-core machines by processing many contexts in parallel.

(C) Furthermore, a large number of additional candidate alignments can be created for each read with only little influence on runtime. Here, ContextMap creates all possible alignments for each read satisfying the maximum mismatch criterion, including e.g. additional split read alignments derived from full read alignments that overlap with a previously identified splice site.

(D) + (E) Resolution of the many ambiguous alignments for each read is performed in steps (D) and (E), first within contexts (D) and subsequently between contexts (E). Both of these resolution steps are based on a scoring scheme that takes into account the number of reads aligned within and around a particular read alignment. If a transcriptome annotation is provided, ContextMap prefers candidate split read alignments corresponding to known junctions. In both (D) and (E) the alignment with the highest support score is chosen for each read instead of simply the alignment with the minimum number of mismatches, resulting in a unique mapping for each read first within each context (step D) and finally across all contexts (E).