About the Software

Authors: Xingzhi Song, Yue Liu, Jiaxin Qu, Richard A. Gibbs, Kim C. Worley

Many gaps in WGS assembled genomes are due to repeats that the whole genome assembly cannot place unambigouously. ATLAS GapFill deals with the repetitive gap assembly problem by using the unique gap-flanking sequences to group reads and convert the problem to a local assembly task. Localizing the assembly reduces the numbers of repeats in the assembly, allows more data to be incorporated, and allows for gaps to be filled.

ATLAS GapFill (1) Identifies gap-associated reads from BWA mapping results for each gap, and assembles each gap locally using different available assemblers (Phrap, Newbler, and Velvet), (2) Compares the locally assembled contigs to the corresponding reference scaffold using Crossmatch, and (3) Fills the gaps of the scaffold with the locally assembled contigs that bridge the gaps.


 (1) System: Unix or Linux operating system (tested on Redhat)
       Cluster queuing software (tested with qsub, bsub and msub)
       Memory greater than 16Gb for each node
 (2) Perl: any version (tested on v5.8.8 built for x86_64-linux-thread-multi)
 (3) Third party tools:
       BWA (test version: 0.5.7)
       Phrap (test version: 0.990329)
       Newbler (test version: MapAsmResearch-04/19/2010)
       Velvet (test version: 1.0.15)
       Crossmatch (test version: 0.990319) 



Version 2.2 (September 2012)


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Carson Jiaxin Qu