SRAssembler

Description

srassembler website  

The SRAssembler repository is the distribution point of our code for selective local assembly of genomic regions matching a homologous query protein or DNA sequence.

SRAssembler (Selective Recursive local Assembler) is a modular pipeline program that can assemble genomic DNA reads into contigs that are homologous to a query DNA or protein sequence. SRAssembler first collects the reads that can be locally aligned to the query sequence and assembles them into contigs. Additional reads are then found by aligning against the contigs assembled in the previous round. This in silico chromosome walking strategy recursively gathers reads that are associated with regions of interest. The gene structures of the final contigs are predicted by spliced alignment and ab initio gene finding programs.

Environment Modules

Run module spider srassembler to find out what environment modules are available for this application.

System Variables

• HPC_SRASSEMBLER_DIR - installation directory
• HPC_SRASSEMBLER_BIN - executable directory

Citation

If you publish research that uses srassembler you have to cite it as follows:

Thomas W. McCarthy, Hsien-Chao Chou, and Volker P. Brendel (2018) SRAssembler: Selective Recursive local Assembly of homologous genomic regions.