aTRAM¶
Description¶
aTRAM ("automated target restricted assembly method") is an iterative assembler that performs reference-guided local de novo assemblies using a variety of available methods. It is well-suited to various tasks where Next-Generation Sequence (NGS) data needs to be queried for gene sequences, such as phylogenomics. The design philosophy is modular and expandable, with support for four de-novo assemblers to date: Velvet, Abyss, Trinity, and Spades. aTRAM 2 is a major overhaul of the aTRAM approach to assembling loci from (NGS) data. The new code has been reimplemented in Python, and the approach to short read library construction is completely revamped, resulting in major performance and assembly improvements.
Environment Modules¶
Run module spider atram to find out what environment modules are available for this application.
Environment Variables¶
Citation¶
If you publish research that uses atram you have to cite it as follows:
Categories¶
math