Graphic of the aTRAM method. A) Formation of the aTRAM database; DNA is sequenced into a paired-end short read dataset (SRD). aTRAM splits the SRD into shards, creates a BLAST formatted database of the first pair and indexes the paired-end for the sequences in each shard. B) In iteration 0 a query sequence in either amino acid or DNA format is queried against the aTRAM formatted database using BLAST. The top-hits and their paired-ends are selected and assembled de novo. In the following iterations the contigs from the previous iteration are queried against the same database using BLAST, the top-hits and paired-ends selected and assembled de novo until the full locus is assembled.