TY - JOUR AU - Allen, Julie M. AU - Huang, Daisie I. AU - Cronk, Quentin C. AU - Johnson, Kevin P. PY - 2015 DA - 2015/03/25 TI - aTRAM - automated target restricted assembly method: a fast method for assembling loci across divergent taxa from next-generation sequencing data JO - BMC Bioinformatics SP - 98 VL - 16 IS - 1 AB - Assembling genes from next-generation sequencing data is not only time consuming but computationally difficult, particularly for taxa without a closely related reference genome. Assembling even a draft genome using de novo approaches can take days, even on a powerful computer, and these assemblies typically require data from a variety of genomic libraries. Here we describe software that will alleviate these issues by rapidly assembling genes from distantly related taxa using a single library of paired-end reads: aTRAM, automated Target Restricted Assembly Method. The aTRAM pipeline uses a reference sequence, BLAST, and an iterative approach to target and locally assemble the genes of interest. SN - 1471-2105 UR - https://doi.org/10.1186/s12859-015-0515-2 DO - 10.1186/s12859-015-0515-2 ID - Allen2015 ER -