Client-server alignment without pre-specified reference genome.
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Abstract
<p>(A) A small random sample of the umapped reads (initially all reads) is taken by the client and sent to the server. (B) In return the server sends a list of hits, or candidate reference sequences for the sample. (C) The client then iterates through the top hits and for each one requests the full genomic sequence from the server after checking that it does not already have a copy of it locally, and calls bowtie2 to build an index for that reference and align all currently unmapped reads to it. The reference for which the most reads map is kept, and unmapped reads remaining are moved back to step (A). The outcome is a list of reference genomes, along with a percentage of the reads iteratively aligning to these references (screenshot in (D)).</p